diff --git a/packages/babel-core/src/transformation/normalize-opts.ts b/packages/babel-core/src/transformation/normalize-opts.ts
index 571d1705530d..50bb169a263b 100644
--- a/packages/babel-core/src/transformation/normalize-opts.ts
+++ b/packages/babel-core/src/transformation/normalize-opts.ts
@@ -2,6 +2,13 @@ import path from "path";
 import type { ResolvedConfig } from "../config/index.ts";
 
 export default function normalizeOptions(config: ResolvedConfig): {} {
+  // TODO: Everything in this function is basically typed as `any`. Improve it.
+
+  // TODO(@nicolo-ribaudo): Currently, soure map's `sources` is generated taking
+  // into account both the options passed to the parser and the options passed
+  // to the generator. If they disagree, both are included. Clean this up, so
+  // that there is a single source of thruth.
+
   const {
     filename,
     cwd,
@@ -15,7 +22,9 @@ export default function normalizeOptions(config: ResolvedConfig): {} {
       ? undefined
       : config.options.moduleRoot,
 
-    sourceFileName = path.basename(filenameRelative),
+    sourceFileName = filenameRelative === "unknown"
+      ? undefined
+      : filenameRelative,
 
     comments = true,
     compact = "auto",
@@ -30,7 +39,10 @@ export default function normalizeOptions(config: ResolvedConfig): {} {
       sourceType:
         path.extname(filenameRelative) === ".mjs" ? "module" : sourceType,
 
-      sourceFileName: filename,
+      // TODO: @babel/parser uses sourceFilename, while @babel/generator and
+      // @babel/core use sourceFileName. Eventualy align them.
+      // https://github.com/babel/babel/pull/13518
+      sourceFilename: sourceFileName,
       plugins: [],
       ...opts.parserOpts,
     },
@@ -51,7 +63,18 @@ export default function normalizeOptions(config: ResolvedConfig): {} {
       sourceMaps,
 
       sourceRoot,
-      sourceFileName,
+      sourceFileName:
+        // If there is no filename, we use `"unknown"` in the source map
+        // `sources` array as a fallback. Due to how @babel/generator works,
+        // if we passed `undefined` there would be no generated mappings.
+        // Additionally, `undefined` isn't JSON-serializable.
+        sourceFileName == null
+          ? "unknown"
+          : sourceRoot == null
+          ? sourceFileName
+          : // @babel/generator will prepend sourceFileName with sourceRoot,
+            // so we need to remove it here.
+            path.relative(sourceRoot, sourceFileName),
       ...opts.generatorOpts,
     },
   };
diff --git a/packages/babel-core/test/api.js b/packages/babel-core/test/api.js
index 79a0d9ae7973..c223313b837a 100644
--- a/packages/babel-core/test/api.js
+++ b/packages/babel-core/test/api.js
@@ -648,14 +648,14 @@ describe("api", function () {
     });
   });
 
-  it("default source map filename", function () {
-    return transformAsync("var a = 10;", {
+  it("default source map filename", async function () {
+    const result = await transformAsync("var a = 10;", {
       cwd: "/some/absolute",
       filename: "/some/absolute/file/path.js",
       sourceMaps: true,
-    }).then(function (result) {
-      expect(result.map.sources).toEqual(["path.js"]);
     });
+
+    expect(result.map.sources).toEqual(["file/path.js"]);
   });
 
   it("code option false", function () {
diff --git a/packages/babel-core/test/fixtures/parse/output-with-filename.json b/packages/babel-core/test/fixtures/parse/output-with-filename.json
new file mode 100644
index 000000000000..591ee626ebe9
--- /dev/null
+++ b/packages/babel-core/test/fixtures/parse/output-with-filename.json
@@ -0,0 +1,339 @@
+{
+  "type": "File",
+  "start": 0,
+  "end": 91,
+  "loc": {
+    "start": {
+      "line": 1,
+      "column": 0,
+      "index": 0
+    },
+    "end": {
+      "line": 7,
+      "column": 0,
+      "index": 91
+    },
+    "filename": "input.js"
+  },
+  "errors": [],
+  "program": {
+    "type": "Program",
+    "start": 0,
+    "end": 91,
+    "loc": {
+      "start": {
+        "line": 1,
+        "column": 0,
+        "index": 0
+      },
+      "end": {
+        "line": 7,
+        "column": 0,
+        "index": 91
+      },
+      "filename": "input.js"
+    },
+    "sourceType": "module",
+    "interpreter": null,
+    "body": [
+      {
+        "type": "ClassDeclaration",
+        "start": 0,
+        "end": 29,
+        "loc": {
+          "start": {
+            "line": 1,
+            "column": 0,
+            "index": 0
+          },
+          "end": {
+            "line": 2,
+            "column": 17,
+            "index": 29
+          },
+          "filename": "input.js"
+        },
+        "decorators": [
+          {
+            "type": "Decorator",
+            "start": 0,
+            "end": 11,
+            "loc": {
+              "start": {
+                "line": 1,
+                "column": 0,
+                "index": 0
+              },
+              "end": {
+                "line": 1,
+                "column": 11,
+                "index": 11
+              },
+              "filename": "input.js"
+            },
+            "expression": {
+              "type": "Identifier",
+              "start": 1,
+              "end": 11,
+              "loc": {
+                "start": {
+                  "line": 1,
+                  "column": 1,
+                  "index": 1
+                },
+                "end": {
+                  "line": 1,
+                  "column": 11,
+                  "index": 11
+                },
+                "filename": "input.js",
+                "identifierName": "annotation"
+              },
+              "name": "annotation"
+            }
+          }
+        ],
+        "id": {
+          "type": "Identifier",
+          "start": 18,
+          "end": 25,
+          "loc": {
+            "start": {
+              "line": 2,
+              "column": 6,
+              "index": 18
+            },
+            "end": {
+              "line": 2,
+              "column": 13,
+              "index": 25
+            },
+            "filename": "input.js",
+            "identifierName": "MyClass"
+          },
+          "name": "MyClass"
+        },
+        "superClass": null,
+        "body": {
+          "type": "ClassBody",
+          "start": 26,
+          "end": 29,
+          "loc": {
+            "start": {
+              "line": 2,
+              "column": 14,
+              "index": 26
+            },
+            "end": {
+              "line": 2,
+              "column": 17,
+              "index": 29
+            },
+            "filename": "input.js"
+          },
+          "body": []
+        }
+      },
+      {
+        "type": "FunctionDeclaration",
+        "start": 31,
+        "end": 90,
+        "loc": {
+          "start": {
+            "line": 4,
+            "column": 0,
+            "index": 31
+          },
+          "end": {
+            "line": 6,
+            "column": 1,
+            "index": 90
+          },
+          "filename": "input.js"
+        },
+        "id": {
+          "type": "Identifier",
+          "start": 40,
+          "end": 50,
+          "loc": {
+            "start": {
+              "line": 4,
+              "column": 9,
+              "index": 40
+            },
+            "end": {
+              "line": 4,
+              "column": 19,
+              "index": 50
+            },
+            "filename": "input.js",
+            "identifierName": "annotation"
+          },
+          "name": "annotation"
+        },
+        "generator": false,
+        "async": false,
+        "params": [
+          {
+            "type": "Identifier",
+            "start": 51,
+            "end": 57,
+            "loc": {
+              "start": {
+                "line": 4,
+                "column": 20,
+                "index": 51
+              },
+              "end": {
+                "line": 4,
+                "column": 26,
+                "index": 57
+              },
+              "filename": "input.js",
+              "identifierName": "target"
+            },
+            "name": "target"
+          }
+        ],
+        "body": {
+          "type": "BlockStatement",
+          "start": 59,
+          "end": 90,
+          "loc": {
+            "start": {
+              "line": 4,
+              "column": 28,
+              "index": 59
+            },
+            "end": {
+              "line": 6,
+              "column": 1,
+              "index": 90
+            },
+            "filename": "input.js"
+          },
+          "body": [
+            {
+              "type": "ExpressionStatement",
+              "start": 64,
+              "end": 88,
+              "loc": {
+                "start": {
+                  "line": 5,
+                  "column": 3,
+                  "index": 64
+                },
+                "end": {
+                  "line": 5,
+                  "column": 27,
+                  "index": 88
+                },
+                "filename": "input.js"
+              },
+              "expression": {
+                "type": "AssignmentExpression",
+                "start": 64,
+                "end": 87,
+                "loc": {
+                  "start": {
+                    "line": 5,
+                    "column": 3,
+                    "index": 64
+                  },
+                  "end": {
+                    "line": 5,
+                    "column": 26,
+                    "index": 87
+                  },
+                  "filename": "input.js"
+                },
+                "operator": "=",
+                "left": {
+                  "type": "MemberExpression",
+                  "start": 64,
+                  "end": 80,
+                  "loc": {
+                    "start": {
+                      "line": 5,
+                      "column": 3,
+                      "index": 64
+                    },
+                    "end": {
+                      "line": 5,
+                      "column": 19,
+                      "index": 80
+                    },
+                    "filename": "input.js"
+                  },
+                  "object": {
+                    "type": "Identifier",
+                    "start": 64,
+                    "end": 70,
+                    "loc": {
+                      "start": {
+                        "line": 5,
+                        "column": 3,
+                        "index": 64
+                      },
+                      "end": {
+                        "line": 5,
+                        "column": 9,
+                        "index": 70
+                      },
+                      "filename": "input.js",
+                      "identifierName": "target"
+                    },
+                    "name": "target"
+                  },
+                  "computed": false,
+                  "property": {
+                    "type": "Identifier",
+                    "start": 71,
+                    "end": 80,
+                    "loc": {
+                      "start": {
+                        "line": 5,
+                        "column": 10,
+                        "index": 71
+                      },
+                      "end": {
+                        "line": 5,
+                        "column": 19,
+                        "index": 80
+                      },
+                      "filename": "input.js",
+                      "identifierName": "annotated"
+                    },
+                    "name": "annotated"
+                  }
+                },
+                "right": {
+                  "type": "BooleanLiteral",
+                  "start": 83,
+                  "end": 87,
+                  "loc": {
+                    "start": {
+                      "line": 5,
+                      "column": 22,
+                      "index": 83
+                    },
+                    "end": {
+                      "line": 5,
+                      "column": 26,
+                      "index": 87
+                    },
+                    "filename": "input.js"
+                  },
+                  "value": true
+                }
+              }
+            }
+          ],
+          "directives": []
+        }
+      }
+    ],
+    "directives": []
+  },
+  "comments": []
+}
diff --git a/packages/babel-core/test/fixtures/parse/output.json b/packages/babel-core/test/fixtures/parse/output.json
index 1a400f953757..1af0d0d0d23c 100644
--- a/packages/babel-core/test/fixtures/parse/output.json
+++ b/packages/babel-core/test/fixtures/parse/output.json
@@ -2,7 +2,6 @@
   "type": "File",
   "start": 0,
   "end": 91,
-  "errors": [],
   "loc": {
     "start": {
       "line": 1,
@@ -15,6 +14,7 @@
       "index": 91
     }
   },
+  "errors": [],
   "program": {
     "type": "Program",
     "start": 0,
@@ -31,8 +31,8 @@
         "index": 91
       }
     },
-    "interpreter": null,
     "sourceType": "module",
+    "interpreter": null,
     "body": [
       {
         "type": "ClassDeclaration",
@@ -270,6 +270,7 @@
                     },
                     "name": "target"
                   },
+                  "computed": false,
                   "property": {
                     "type": "Identifier",
                     "start": 71,
@@ -288,8 +289,7 @@
                       "identifierName": "annotated"
                     },
                     "name": "annotated"
-                  },
-                  "computed": false
+                  }
                 },
                 "right": {
                   "type": "BooleanLiteral",
diff --git a/packages/babel-core/test/parse.js b/packages/babel-core/test/parse.js
index eeec4ce7869d..dcfa1813d4e8 100644
--- a/packages/babel-core/test/parse.js
+++ b/packages/babel-core/test/parse.js
@@ -18,7 +18,7 @@ function fixture(...args) {
 describe("parseSync", function () {
   it("should parse using configuration from .babelrc when a filename is provided", function () {
     const input = fs.readFileSync(fixture("input.js"), "utf8");
-    const output = require(fixture("output"));
+    const output = require(fixture("output-with-filename.json"));
 
     const result = parseSync(input, {
       filename: fixture("input.js"),