diff --git a/src/api-extractor.ts b/src/api-extractor.ts
index 618615bf4..df4b40607 100644
--- a/src/api-extractor.ts
+++ b/src/api-extractor.ts
@@ -9,6 +9,7 @@ import {
   getApiExtractor,
   removeFiles,
   toAbsolutePath,
+  writeFileSync,
 } from './utils'
 import type {
   ExperimentalDtsConfig,
@@ -22,6 +23,7 @@ import type {
   IExtractorConfigPrepareOptions,
 } from '@microsoft/api-extractor'
 import type { InputOption } from 'rollup'
+import { formatAggregationExports, formatDistributionExports, type ExportDeclaration } from "./exports"
 
 const logger = createLogger()
 
@@ -86,13 +88,7 @@ function rollupDtsFile(
 
 async function rollupDtsFiles(
   options: NormalizedOptions,
-  exports: {
-    /**
-     * **Source file name** to **Output file name** mapping.
-     * (`src/index.ts` \=> `.tsup/declaration/index.d.ts`)
-     */
-    fileMapping: Map<string, string>
-  },
+  exports: ExportDeclaration[],
   format: Format,
 ) {
   if (!options.experimentalDts || !options.experimentalDts?.entry) {
@@ -108,6 +104,32 @@ async function rollupDtsFiles(
   const dtsExtension = defaultOutExtension({ format, pkgType: pkg.type }).dts
   const tsconfig = options.tsconfig || 'tsconfig.json'
 
+  let dtsInputFilePath = path.join(
+    declarationDir,
+    `_tsup-dts-aggregation${dtsExtension}`,
+  )
+  // @microsoft/api-extractor doesn't support `.d.mts` and `.d.cts` file as a
+  // entrypoint yet. So we replace the extension here as a temporary workaround.
+  //
+  // See the issue for more details:
+  // https://github.com/microsoft/rushstack/pull/4196
+  dtsInputFilePath = dtsInputFilePath
+    .replace(/\.d\.mts$/, '.dmts.d.ts')
+    .replace(/\.d\.cts$/, '.dcts.d.ts')
+
+  const dtsOutputFilePath = path.join(outDir, `_tsup-dts-rollup${dtsExtension}`)
+
+  writeFileSync(
+    dtsInputFilePath,
+    formatAggregationExports(exports, declarationDir),
+  )
+
+  rollupDtsFile(
+    dtsInputFilePath,
+    dtsOutputFilePath,
+    tsconfig,
+  )
+
   for (let [out, sourceFileName] of Object.entries(
     options.experimentalDts.entry,
   )) {
@@ -142,14 +164,15 @@ async function rollupDtsFiles(
      */
     const outFileName = path.join(outDir, out + dtsExtension)
 
-    /**
-     * **Input file path** (`.tsup/declaration/index.d.ts`)
-     */
-    const inputFilePath =
-      exports.fileMapping.get(sourceFileName) ||
-      `${path.join(declarationDir, out)}.d.ts`
+    // Find all declarations that are exported from the current source file
+    const currentExports = exports.filter(
+      (declaration) => declaration.sourceFileName === sourceFileName,
+    )
 
-    rollupDtsFile(inputFilePath, outFileName, tsconfig)
+    writeFileSync(
+      outFileName,
+      formatDistributionExports(currentExports, outFileName, dtsOutputFilePath),
+    )
   }
 }
 
@@ -161,13 +184,7 @@ async function cleanDtsFiles(options: NormalizedOptions) {
 
 export async function runDtsRollup(
   options: NormalizedOptions,
-  exports?: {
-    /**
-     * **Source file name** to **Output file name** mapping.
-     * (`src/index.ts` \=> `.tsup/declaration/index.d.ts`)
-     */
-    fileMapping: Map<string, string>
-  },
+  exports?: ExportDeclaration[],
 ) {
   try {
     const start = Date.now()
diff --git a/src/tsc.ts b/src/tsc.ts
index 921d2b8b1..3b1aa387d 100644
--- a/src/tsc.ts
+++ b/src/tsc.ts
@@ -198,13 +198,7 @@ function emit(compilerOptions?: any, tsconfig?: string) {
   )
 
   const fileMapping = emitDtsFiles(program, host)
-  return {
-    /**
-     * **Source file name** to **Output file name** mapping.
-     * (`src/index.ts` \=> `.tsup/declaration/index.d.ts`)
-     */
-    fileMapping,
-  }
+  return getExports(program, fileMapping)
 }
 
 export function runTypeScriptCompiler(options: NormalizedOptions) {