diff --git a/docs/config/index.md b/docs/config/index.md
index d62f1ca06f55..fc4de4cb9eaf 100644
--- a/docs/config/index.md
+++ b/docs/config/index.md
@@ -1313,6 +1313,18 @@ Generate coverage report even when tests fail.
 
 Collect coverage of files outside the [project `root`](#root).
 
+#### coverage.excludeAfterRemap <Version>2.1.0</Version> {#coverage-exclude-after-remap}
+
+- **Type:** `boolean`
+- **Default:** `false`
+- **Available for providers:** `'v8' | 'istanbul'`
+- **CLI:** `--coverage.excludeAfterRemap`, `--coverage.excludeAfterRemap=false`
+
+Apply exclusions again after coverage has been remapped to original sources.
+This is useful when your source files are transpiled and may contain source maps of non-source files.
+
+Use this option when you are seeing files that show up in report even if they match your `coverage.exclude` patterns.
+
 #### coverage.skipFull
 
 - **Type:** `boolean`
diff --git a/packages/coverage-istanbul/src/provider.ts b/packages/coverage-istanbul/src/provider.ts
index 98ed3df75bb1..0dd865631633 100644
--- a/packages/coverage-istanbul/src/provider.ts
+++ b/packages/coverage-istanbul/src/provider.ts
@@ -109,9 +109,7 @@ export class IstanbulCoverageProvider extends BaseCoverageProvider implements Co
         lines: config.thresholds['100'] ? 100 : config.thresholds.lines,
         branches: config.thresholds['100'] ? 100 : config.thresholds.branches,
         functions: config.thresholds['100'] ? 100 : config.thresholds.functions,
-        statements: config.thresholds['100']
-          ? 100
-          : config.thresholds.statements,
+        statements: config.thresholds['100'] ? 100 : config.thresholds.statements,
       },
     }
 
@@ -292,6 +290,10 @@ export class IstanbulCoverageProvider extends BaseCoverageProvider implements Co
       coverageMap.merge(await transformCoverage(uncoveredCoverage))
     }
 
+    if (this.options.excludeAfterRemap) {
+      coverageMap.filter(filename => this.testExclude.shouldInstrument(filename))
+    }
+
     return coverageMap
   }
 
diff --git a/packages/coverage-v8/src/provider.ts b/packages/coverage-v8/src/provider.ts
index 532b9d437e08..b6b0f8708b73 100644
--- a/packages/coverage-v8/src/provider.ts
+++ b/packages/coverage-v8/src/provider.ts
@@ -253,6 +253,10 @@ export class V8CoverageProvider extends BaseCoverageProvider implements Coverage
       coverageMap.merge(await transformCoverage(converted))
     }
 
+    if (this.options.excludeAfterRemap) {
+      coverageMap.filter(filename => this.testExclude.shouldInstrument(filename))
+    }
+
     return coverageMap
   }
 
diff --git a/packages/vitest/src/defaults.ts b/packages/vitest/src/defaults.ts
index f95ad627a036..07bc35a37910 100644
--- a/packages/vitest/src/defaults.ts
+++ b/packages/vitest/src/defaults.ts
@@ -75,6 +75,7 @@ export const coverageConfigDefaults: ResolvedCoverageOptions = {
     '.marko',
   ],
   allowExternal: false,
+  excludeAfterRemap: false,
   ignoreEmptyLines: true,
   processingConcurrency: Math.min(
     20,
diff --git a/packages/vitest/src/node/types/coverage.ts b/packages/vitest/src/node/types/coverage.ts
index a5d18dd152e2..993ed20cee92 100644
--- a/packages/vitest/src/node/types/coverage.ts
+++ b/packages/vitest/src/node/types/coverage.ts
@@ -251,6 +251,18 @@ export interface BaseCoverageOptions {
    */
   allowExternal?: boolean
 
+  /**
+   * Apply exclusions again after coverage has been remapped to original sources.
+   * This is useful when your source files are transpiled and may contain source maps
+   * of non-source files.
+   *
+   * Use this option when you are seeing files that show up in report even if they
+   * match your `coverage.exclude` patterns.
+   *
+   * @default false
+   */
+  excludeAfterRemap?: boolean
+
   /**
    * Concurrency limit used when processing the coverage results.
    * Defaults to `Math.min(20, os.availableParallelism?.() ?? os.cpus().length)`
diff --git a/test/coverage-test/test/exclude-after-remap.test.ts b/test/coverage-test/test/exclude-after-remap.test.ts
new file mode 100644
index 000000000000..087567484564
--- /dev/null
+++ b/test/coverage-test/test/exclude-after-remap.test.ts
@@ -0,0 +1,71 @@
+import { expect } from 'vitest'
+import { coverageTest, normalizeURL, readCoverageMap, runVitest, test } from '../utils.js'
+import * as transpiled from '../fixtures/src/pre-bundle/bundle.js'
+
+test('{ excludeAfterRemap: true } should exclude files that come up after remapping', async () => {
+  await runVitest({
+    include: [normalizeURL(import.meta.url)],
+    coverage: {
+      include: ['fixtures/src/**'],
+      exclude: ['fixtures/src/pre-bundle/second.ts'],
+      excludeAfterRemap: true,
+      reporter: 'json',
+      all: false,
+    },
+  })
+
+  const coverageMap = await readCoverageMap()
+  const files = coverageMap.files()
+
+  expect(files).toMatchInlineSnapshot(`
+    [
+      "<process-cwd>/fixtures/src/pre-bundle/first.ts",
+    ]
+  `)
+})
+
+test('{ excludeAfterRemap: false } should not exclude files that come up after remapping', async () => {
+  await runVitest({
+    include: [normalizeURL(import.meta.url)],
+    coverage: {
+      include: ['fixtures/src/**'],
+      exclude: ['fixtures/src/pre-bundle/second.ts'],
+      reporter: 'json',
+      all: false,
+    },
+  })
+
+  const coverageMap = await readCoverageMap()
+  const files = coverageMap.files()
+
+  expect(files).toMatchInlineSnapshot(`
+    [
+      "<process-cwd>/fixtures/src/pre-bundle/first.ts",
+      "<process-cwd>/fixtures/src/pre-bundle/second.ts",
+    ]
+  `)
+})
+
+test('{ excludeAfterRemap: true } should exclude uncovered files that come up after remapping', async () => {
+  await runVitest({
+    include: ['fixtures/test/math.test.ts'],
+    coverage: {
+      include: ['fixtures/src/pre-bundle/**'],
+      exclude: ['fixtures/src/pre-bundle/second.ts'],
+      excludeAfterRemap: true,
+      reporter: 'json',
+      all: true,
+    },
+  })
+
+  const coverageMap = await readCoverageMap()
+  const files = coverageMap.files()
+
+  expect(files).contains('<process-cwd>/fixtures/src/pre-bundle/first.ts')
+  expect(files).not.contains('<process-cwd>/fixtures/src/pre-bundle/second.ts')
+})
+
+coverageTest('run bundled sources', () => {
+  expect(transpiled.first.covered()).toBe('First')
+  expect(transpiled.second.covered()).toBe('Second')
+})