diff --git a/lib/rules/spaced-comment.js b/lib/rules/spaced-comment.js
index 958bb2c6444..daf56cd6bb4 100644
--- a/lib/rules/spaced-comment.js
+++ b/lib/rules/spaced-comment.js
@@ -249,7 +249,8 @@ module.exports = {
                 beginRegex: requireSpace ? createAlwaysStylePattern(markers, exceptions) : createNeverStylePattern(markers),
                 endRegex: balanced && requireSpace ? new RegExp(`${createExceptionsPattern(exceptions)}$`, "u") : new RegExp(endNeverPattern, "u"),
                 hasExceptions: exceptions.length > 0,
-                markers: new RegExp(`^(${markers.map(escape).join("|")})`, "u")
+                captureMarker: new RegExp(`^(${markers.map(escape).join("|")})`, "u"),
+                markers: new Set(markers)
             };
 
             return rule;
@@ -322,8 +323,8 @@ module.exports = {
                 rule = styleRules[type],
                 commentIdentifier = type === "block" ? "/*" : "//";
 
-            // Ignores empty comments.
-            if (node.value.length === 0) {
+            // Ignores empty comments and comments that consist only of a marker.
+            if (node.value.length === 0 || rule.markers.has(node.value)) {
                 return;
             }
 
@@ -333,7 +334,7 @@ module.exports = {
             // Checks.
             if (requireSpace) {
                 if (!beginMatch) {
-                    const hasMarker = rule.markers.exec(node.value);
+                    const hasMarker = rule.captureMarker.exec(node.value);
                     const marker = hasMarker ? commentIdentifier + hasMarker[0] : commentIdentifier;
 
                     if (rule.hasExceptions) {
diff --git a/tests/lib/rules/spaced-comment.js b/tests/lib/rules/spaced-comment.js
index fd6b2e51098..ee28203d10e 100644
--- a/tests/lib/rules/spaced-comment.js
+++ b/tests/lib/rules/spaced-comment.js
@@ -304,6 +304,44 @@ ruleTester.run("spaced-comment", rule, {
         {
             code: "/***\u2028*/",
             options: ["always", { exceptions: ["*"] }]
+        },
+
+        // ignore marker-only comments, https://github.com/eslint/eslint/issues/12036
+        {
+            code: "//#endregion",
+            options: ["always", { line: { markers: ["#endregion"] } }]
+        },
+        {
+            code: "/*foo*/",
+            options: ["always", { block: { markers: ["foo"] } }]
+        },
+        {
+            code: "/*foo*/",
+            options: ["always", { block: { markers: ["foo"], balanced: true } }]
+        },
+        {
+            code: "/*foo*/ /*bar*/",
+            options: ["always", { markers: ["foo", "bar"] }]
+        },
+        {
+            code: "//foo\n//bar",
+            options: ["always", { markers: ["foo", "bar"] }]
+        },
+        {
+            code: "/* foo */",
+            options: ["never", { markers: [" foo "] }]
+        },
+        {
+            code: "// foo ",
+            options: ["never", { markers: [" foo "] }]
+        },
+        {
+            code: "//*", // "*" is a marker by default
+            options: ["always"]
+        },
+        {
+            code: "/***/", // "*" is a marker by default
+            options: ["always"]
         }
     ],
 
@@ -586,6 +624,65 @@ ruleTester.run("spaced-comment", rule, {
             output: null,
             options: ["never"],
             errors: 1
+        },
+
+        // not a marker-only comment, regression tests for https://github.com/eslint/eslint/issues/12036
+        {
+            code: "//#endregionfoo",
+            output: "//#endregion foo",
+            options: ["always", { line: { markers: ["#endregion"] } }],
+            errors: [{
+                message: "Expected space or tab after '//#endregion' in comment.",
+                type: "Line"
+            }]
+        },
+        {
+            code: "/*#endregion*/",
+            output: "/* #endregion*/", // not an allowed marker for block comments
+            options: ["always", { line: { markers: ["#endregion"] } }],
+            errors: [{
+                message: "Expected space or tab after '/*' in comment.",
+                type: "Block"
+            }]
+        },
+        {
+            code: "/****/",
+            output: "/** **/",
+            options: ["always"],
+            errors: [{
+                message: "Expected space or tab after '/**' in comment.",
+                type: "Block"
+            }]
+        },
+        {
+            code: "/****/",
+            output: "/** * */",
+            options: ["always", { block: { balanced: true } }],
+            errors: [
+                {
+                    message: "Expected space or tab after '/**' in comment.",
+                    type: "Block"
+                },
+                {
+                    message: "Expected space or tab before '*/' in comment.",
+                    type: "Block"
+                }
+            ]
+        },
+        {
+            code: "/* foo */",
+            output: "/*foo*/",
+            options: ["never", { block: { markers: ["foo"], balanced: true } }], // not " foo "
+            errors: [
+                {
+                    message: "Unexpected space or tab after '/*' in comment.",
+                    type: "Block"
+                },
+                {
+                    message: "Unexpected space or tab before '*/' in comment.",
+                    type: "Block"
+                }
+            ]
         }
     ]