diff --git a/lib/config/flat-config-schema.js b/lib/config/flat-config-schema.js
index 3b6612b4984..55546134ec3 100644
--- a/lib/config/flat-config-schema.js
+++ b/lib/config/flat-config-schema.js
@@ -62,13 +62,17 @@ function isUndefined(value) {
     return typeof value === "undefined";
 }
 
+// A unique empty object to be used internally as a mapping key in `deepMerge`.
+const EMPTY_OBJECT = {};
+
 /**
  * Deeply merges two objects.
  * @param {Object} first The base object.
- * @param {Object} second The overrides object.
+ * @param {any} second The overrides value.
+ * @param {Map<string, Map<string, Object>>} [mergeMap] Maps the combination of first and second arguments to a merged result.
  * @returns {Object} An object with properties from both first and second.
  */
-function deepMerge(first = {}, second = {}) {
+function deepMerge(first, second = {}, mergeMap = new Map()) {
 
     /*
      * If the second value is an array, just return it. We don't merge
@@ -78,8 +82,23 @@ function deepMerge(first = {}, second = {}) {
         return second;
     }
 
+    let secondMergeMap = mergeMap.get(first);
+
+    if (secondMergeMap) {
+        const result = secondMergeMap.get(second);
+
+        if (result) {
+
+            // If this combination of first and second arguments has been already visited, return the previously created result.
+            return result;
+        }
+    } else {
+        secondMergeMap = new Map();
+        mergeMap.set(first, secondMergeMap);
+    }
+
     /*
-     * First create a result object where properties from the second object
+     * First create a result object where properties from the second value
      * overwrite properties from the first. This sets up a baseline to use
      * later rather than needing to inspect and change every property
      * individually.
@@ -89,6 +108,9 @@ function deepMerge(first = {}, second = {}) {
         ...second
     };
 
+    // Store the pending result for this combination of first and second arguments.
+    secondMergeMap.set(second, result);
+
     for (const key of Object.keys(second)) {
 
         // avoid hairy edge case
@@ -100,13 +122,10 @@ function deepMerge(first = {}, second = {}) {
         const secondValue = second[key];
 
         if (isNonNullObject(firstValue)) {
-            result[key] = deepMerge(firstValue, secondValue);
+            result[key] = deepMerge(firstValue, secondValue, mergeMap);
         } else if (isUndefined(firstValue)) {
             if (isNonNullObject(secondValue)) {
-                result[key] = deepMerge(
-                    Array.isArray(secondValue) ? [] : {},
-                    secondValue
-                );
+                result[key] = deepMerge(EMPTY_OBJECT, secondValue, mergeMap);
             } else if (!isUndefined(secondValue)) {
                 result[key] = secondValue;
             }
diff --git a/tests/lib/config/flat-config-schema.js b/tests/lib/config/flat-config-schema.js
new file mode 100644
index 00000000000..1cde41ab16b
--- /dev/null
+++ b/tests/lib/config/flat-config-schema.js
@@ -0,0 +1,228 @@
+/**
+ * @fileoverview Tests for flatConfigSchema
+ * @author Francesco Trotta
+ */
+
+"use strict";
+
+const { flatConfigSchema } = require("../../../lib/config/flat-config-schema");
+const { assert } = require("chai");
+
+describe("merge", () => {
+
+    const { merge } = flatConfigSchema.settings;
+
+    it("merges two objects", () => {
+        const first = { foo: 42 };
+        const second = { bar: "baz" };
+        const result = merge(first, second);
+
+        assert.deepStrictEqual(result, { ...first, ...second });
+    });
+
+    it("overrides an object with an array", () => {
+        const first = { foo: 42 };
+        const second = ["bar", "baz"];
+        const result = merge(first, second);
+
+        assert.strictEqual(result, second);
+    });
+
+    it("merges an array with an object", () => {
+        const first = ["foo", "bar"];
+        const second = { baz: 42 };
+        const result = merge(first, second);
+
+        assert.deepStrictEqual(result, { 0: "foo", 1: "bar", baz: 42 });
+    });
+
+    it("overrides an array with another array", () => {
+        const first = ["foo", "bar"];
+        const second = ["baz", "qux"];
+        const result = merge(first, second);
+
+        assert.strictEqual(result, second);
+    });
+
+    it("returns an emtpy object if both values are undefined", () => {
+        const result = merge(void 0, void 0);
+
+        assert.deepStrictEqual(result, {});
+    });
+
+    it("returns an object equal to the first one if the second one is undefined", () => {
+        const first = { foo: 42, bar: "baz" };
+        const result = merge(first, void 0);
+
+        assert.deepStrictEqual(result, first);
+        assert.notStrictEqual(result, first);
+    });
+
+    it("returns an object equal to the second one if the first one is undefined", () => {
+        const second = { foo: 42, bar: "baz" };
+        const result = merge(void 0, second);
+
+        assert.deepStrictEqual(result, second);
+        assert.notStrictEqual(result, second);
+    });
+
+    it("merges two objects in a property", () => {
+        const first = { foo: { bar: "baz" } };
+        const second = { foo: { qux: 42 } };
+        const result = merge(first, second);
+
+        assert.deepStrictEqual(result, { foo: { bar: "baz", qux: 42 } });
+    });
+
+    it("does not override a value in a property with undefined", () => {
+        const first = { foo: { bar: "baz" } };
+        const second = { foo: void 0 };
+        const result = merge(first, second);
+
+        assert.deepStrictEqual(result, first);
+        assert.notStrictEqual(result, first);
+    });
+
+    it("does not change the prototype of a merged object", () => {
+        const first = { foo: 42 };
+        const second = { bar: "baz", ["__proto__"]: { qux: true } };
+        const result = merge(first, second);
+
+        assert.strictEqual(Object.getPrototypeOf(result), Object.prototype);
+    });
+
+    it("does not merge the '__proto__' property", () => {
+        const first = { ["__proto__"]: { foo: 42 } };
+        const second = { ["__proto__"]: { bar: "baz" } };
+        const result = merge(first, second);
+
+        assert.deepStrictEqual(result, second);
+        assert.notStrictEqual(result, second);
+    });
+
+    it("throws an error if a value in a property is overriden with null", () => {
+        const first = { foo: { bar: "baz" } };
+        const second = { foo: null };
+
+        assert.throws(() => merge(first, second), TypeError);
+    });
+
+    it("does not override a value in a property with a primitive", () => {
+        const first = { foo: { bar: "baz" } };
+        const second = { foo: 42 };
+        const result = merge(first, second);
+
+        assert.deepStrictEqual(result, first);
+        assert.notStrictEqual(result, first);
+    });
+
+    it("merges an object in a property with a string", () => {
+        const first = { foo: { bar: "baz" } };
+        const second = { foo: "qux" };
+        const result = merge(first, second);
+
+        assert.deepStrictEqual(result, { foo: { 0: "q", 1: "u", 2: "x", bar: "baz" } });
+    });
+
+    it("merges objects with self-references", () => {
+        const first = { foo: 42 };
+
+        first.first = first;
+        const second = { bar: "baz" };
+
+        second.second = second;
+        const result = merge(first, second);
+
+        assert.strictEqual(result.first, first);
+        assert.deepStrictEqual(result.second, second);
+
+        const expected = { foo: 42, bar: "baz" };
+
+        expected.first = first;
+        expected.second = second;
+        assert.deepStrictEqual(result, expected);
+    });
+
+    it("merges objects with overlapping self-references", () => {
+        const first = { foo: 42 };
+
+        first.reference = first;
+        const second = { bar: "baz" };
+
+        second.reference = second;
+
+        const result = merge(first, second);
+
+        assert.strictEqual(result.reference, result);
+
+        const expected = { foo: 42, bar: "baz" };
+
+        expected.reference = expected;
+        assert.deepStrictEqual(result, expected);
+    });
+
+    it("merges objects with cross-references", () => {
+        const first = { foo: 42 };
+        const second = { bar: "baz" };
+
+        first.second = second;
+        second.first = first;
+
+        const result = merge(first, second);
+
+        assert.deepStrictEqual(result.first, first);
+        assert.strictEqual(result.second, second);
+
+        const expected = { foo: 42, bar: "baz" };
+
+        expected.first = first;
+        expected.second = second;
+        assert.deepStrictEqual(result, expected);
+    });
+
+    it("merges objects with overlapping cross-references", () => {
+        const first = { foo: 42 };
+        const second = { bar: "baz" };
+
+        first.reference = second;
+        second.reference = first;
+
+        const result = merge(first, second);
+
+        assert.strictEqual(result, result.reference.reference);
+
+        const expected = { foo: 42, bar: "baz", reference: { foo: 42, bar: "baz" } };
+
+        expected.reference.reference = expected;
+        assert.deepStrictEqual(result, expected);
+    });
+
+    it("produces the same results for the same combinations of property values", () => {
+        const firstCommon = { foo: 42 };
+        const secondCommon = { bar: "baz" };
+        const first = {
+            a: firstCommon,
+            b: firstCommon,
+            c: { foo: "different" },
+            d: firstCommon
+        };
+        const second = {
+            a: secondCommon,
+            b: { bar: "something else" },
+            c: secondCommon,
+            d: secondCommon
+        };
+        const result = merge(first, second);
+
+        assert.deepStrictEqual(result.a, result.d);
+
+        const expected = {
+            a: { foo: 42, bar: "baz" },
+            b: { foo: 42, bar: "something else" },
+            c: { foo: "different", bar: "baz" },
+            d: { foo: 42, bar: "baz" }
+        };
+
+        assert.deepStrictEqual(result, expected);
+    });
+});
diff --git a/tests/lib/eslint/flat-eslint.js b/tests/lib/eslint/flat-eslint.js
index d71da6936e9..ee417830788 100644
--- a/tests/lib/eslint/flat-eslint.js
+++ b/tests/lib/eslint/flat-eslint.js
@@ -6322,6 +6322,72 @@ describe("FlatESLint", () => {
         });
     }
 
+    describe("config with circular references", () => {
+        it("in 'settings'", async () => {
+            let resolvedSettings = null;
+
+            const circular = {};
+
+            circular.self = circular;
+
+            const eslint = new FlatESLint({
+                overrideConfigFile: true,
+                baseConfig: {
+                    settings: {
+                        sharedData: circular
+                    },
+                    rules: {
+                        "test-plugin/test-rule": 1
+                    }
+                },
+                plugins: {
+                    "test-plugin": {
+                        rules: {
+                            "test-rule": {
+                                create(context) {
+                                    resolvedSettings = context.settings;
+                                    return { };
+                                }
+                            }
+                        }
+                    }
+                }
+            });
+
+            await eslint.lintText("debugger;");
+
+            assert.deepStrictEqual(resolvedSettings.sharedData, circular);
+        });
+
+        it("in 'parserOptions'", async () => {
+            let resolvedParserOptions = null;
+
+            const circular = {};
+
+            circular.self = circular;
+
+            const eslint = new FlatESLint({
+                overrideConfigFile: true,
+                baseConfig: {
+                    languageOptions: {
+                        parser: {
+                            parse(text, parserOptions) {
+                                resolvedParserOptions = parserOptions;
+                            }
+                        },
+                        parserOptions: {
+                            testOption: circular
+                        }
+                    }
+                }
+            });
+
+            await eslint.lintText("debugger;");
+
+            assert.deepStrictEqual(resolvedParserOptions.testOption, circular);
+        });
+    });
+
 });
 
 describe("shouldUseFlatConfig", () => {