diff --git a/modules/build/src/main/scala/scala/build/preprocessing/SheBang.scala b/modules/build/src/main/scala/scala/build/preprocessing/SheBang.scala
index 3b1b29fb56..46dcfb3a8f 100644
--- a/modules/build/src/main/scala/scala/build/preprocessing/SheBang.scala
+++ b/modules/build/src/main/scala/scala/build/preprocessing/SheBang.scala
@@ -7,6 +7,19 @@ object SheBang {
 
   def isShebangScript(content: String): Boolean = sheBangRegex.unanchored.matches(content)
 
+  /** Returns the shebang section and the content without the shebang section */
+  def partitionOnShebangSection(content: String): (String, String) =
+    if (content.startsWith("#!")) {
+      val regexMatch = sheBangRegex.findFirstMatchIn(content)
+      regexMatch match {
+        case Some(firstMatch) =>
+          (firstMatch.toString(), content.replace(firstMatch.toString(), ""))
+        case None => ("", content)
+      }
+    }
+    else
+      ("", content)
+
   def ignoreSheBangLines(content: String): (String, Boolean) =
     if (content.startsWith("#!")) {
       val regexMatch = sheBangRegex.findFirstMatchIn(content)
diff --git a/modules/cli/src/main/scala/scala/cli/commands/fix/Fix.scala b/modules/cli/src/main/scala/scala/cli/commands/fix/Fix.scala
index d130d7a8cb..fd0feeade1 100644
--- a/modules/cli/src/main/scala/scala/cli/commands/fix/Fix.scala
+++ b/modules/cli/src/main/scala/scala/cli/commands/fix/Fix.scala
@@ -148,9 +148,9 @@ object Fix extends ScalaCommand[FixOptions] {
     val logger = loggingUtilities.logger
 
     val fromPaths = sources.paths.map { (path, _) =>
-      val content = os.read(path).toCharArray
+      val (_, content) = SheBang.partitionOnShebangSection(os.read(path))
       logger.debug(s"Extracting directives from ${loggingUtilities.relativePath(path)}")
-      ExtractedDirectives.from(content, Right(path), logger, _ => None).orExit(logger)
+      ExtractedDirectives.from(content.toCharArray, Right(path), logger, _ => None).orExit(logger)
     }
 
     val fromInMemory = sources.inMemory.map { inMem =>
@@ -158,7 +158,7 @@ object Fix extends ScalaCommand[FixOptions] {
       val content = originOrPath match {
         case Right(path) =>
           logger.debug(s"Extracting directives from ${loggingUtilities.relativePath(path)}")
-          os.read(path).toCharArray
+          os.read(path)
         case Left(origin) =>
           logger.debug(s"Extracting directives from $origin")
           inMem.wrapperParamsOpt match {
@@ -166,12 +166,19 @@ object Fix extends ScalaCommand[FixOptions] {
             case Some(wrapperParams) => String(inMem.content)
                 .linesWithSeparators
                 .drop(wrapperParams.topWrapperLineCount)
-                .mkString.toCharArray
-            case None => inMem.content.map(_.toChar)
+                .mkString
+            case None => String(inMem.content)
           }
       }
 
-      ExtractedDirectives.from(content, originOrPath, logger, _ => None).orExit(logger)
+      val (_, contentWithNoShebang) = SheBang.partitionOnShebangSection(content)
+
+      ExtractedDirectives.from(
+        contentWithNoShebang.toCharArray,
+        originOrPath,
+        logger,
+        _ => None
+      ).orExit(logger)
     }
 
     fromPaths ++ fromInMemory
@@ -244,8 +251,16 @@ object Fix extends ScalaCommand[FixOptions] {
   ): Unit = {
     position match {
       case Some(Position.File(Right(path), _, _, offset)) =>
-        val keepLines    = toKeep.mkString("", newLine, newLine * 2)
-        val newContents  = keepLines + os.read(path).drop(offset).stripLeading()
+        val (shebangSection, strippedContent) = SheBang.partitionOnShebangSection(os.read(path))
+
+        def ignoreOrAddNewLine(str: String) = if str.isBlank then "" else str + newLine
+
+        val keepLines = ignoreOrAddNewLine(shebangSection) + ignoreOrAddNewLine(toKeep.mkString(
+          "",
+          newLine,
+          newLine
+        ))
+        val newContents  = keepLines + strippedContent.drop(offset).stripLeading()
         val relativePath = loggingUtilities.relativePath(path)
 
         loggingUtilities.logger.message(s"Removing directives from $relativePath")
diff --git a/modules/integration/src/test/scala/scala/cli/integration/FixTests.scala b/modules/integration/src/test/scala/scala/cli/integration/FixTests.scala
index c42c59ef28..48a37932a0 100644
--- a/modules/integration/src/test/scala/scala/cli/integration/FixTests.scala
+++ b/modules/integration/src/test/scala/scala/cli/integration/FixTests.scala
@@ -73,6 +73,65 @@ class FixTests extends ScalaCliSuite {
     }
   }
 
+  test("fix script with shebang") {
+    val mainFileName = "main.sc"
+    val inputs = TestInputs(
+      os.rel / mainFileName ->
+        s"""#!/usr/bin/env -S scala-cli shebang
+           |
+           |//> using objectWrapper
+           |//> using dep com.lihaoyi::os-lib:0.9.1 com.lihaoyi::upickle:3.1.2
+           |
+           |println(os.pwd)
+           |""".stripMargin,
+      os.rel / projectFileName ->
+        s"""//> using lib "com.lihaoyi::pprint:0.6.6"
+           |""".stripMargin
+    )
+
+    inputs.fromRoot { root =>
+
+      val fixOutput = os.proc(TestUtil.cli, "--power", "fix", ".", "-v", "-v", extraOptions)
+        .call(cwd = root, mergeErrIntoOut = true).out.trim()
+
+      assertNoDiff(
+        fixOutput,
+        """Extracting directives from project.scala
+          |Extracting directives from main.sc
+          |Removing directives from project.scala
+          |Removing directives from main.sc""".stripMargin
+      )
+
+      val projectFileContents = os.read(root / projectFileName)
+      val mainFileContents    = os.read(root / mainFileName)
+
+      assertNoDiff(
+        projectFileContents,
+        """// Main
+          |//> using objectWrapper
+          |
+          |//> using dependency "com.lihaoyi::os-lib:0.9.1"
+          |//> using dependency "com.lihaoyi::pprint:0.6.6"
+          |//> using dependency "com.lihaoyi::upickle:3.1.2"
+          |
+          |""".stripMargin
+      )
+
+      assertNoDiff(
+        mainFileContents,
+        """#!/usr/bin/env -S scala-cli shebang
+          |
+          |println(os.pwd)
+          |""".stripMargin
+      )
+
+      val runProc = os.proc(TestUtil.cli, "--power", "compile", ".", extraOptions)
+        .call(cwd = root, stderr = os.Pipe)
+
+      expect(!runProc.err.trim.contains("Using directives detected in multiple files"))
+    }
+  }
+
   test("fix with test scope") {
     val mainSubPath = os.rel / "src" / "Main.scala"
     val testSubPath = os.rel / "test" / "MyTests.scala"