diff --git a/loader/spring-boot-jarmode-tools/src/main/java/org/springframework/boot/jarmode/tools/ExtractCommand.java b/loader/spring-boot-jarmode-tools/src/main/java/org/springframework/boot/jarmode/tools/ExtractCommand.java
index 41fc37b57a0..988c52af554 100644
--- a/loader/spring-boot-jarmode-tools/src/main/java/org/springframework/boot/jarmode/tools/ExtractCommand.java
+++ b/loader/spring-boot-jarmode-tools/src/main/java/org/springframework/boot/jarmode/tools/ExtractCommand.java
@@ -26,6 +26,7 @@ import java.io.OutputStream;
 import java.io.PrintStream;
 import java.io.UncheckedIOException;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.nio.file.attribute.BasicFileAttributeView;
 import java.nio.file.attribute.BasicFileAttributes;
 import java.nio.file.attribute.FileTime;
@@ -57,6 +58,7 @@ import org.springframework.util.StringUtils;
  * The {@code 'extract'} tools command.
  *
  * @author Moritz Halbritter
+ * @author Dongliang Xie
  */
 class ExtractCommand extends Command {
 
@@ -363,14 +365,18 @@ class ExtractCommand extends Command {
 	}
 
 	private static File assertFileIsContainedInDirectory(File directory, File file, String name) throws IOException {
-		String canonicalOutputPath = directory.getCanonicalPath() + File.separator;
-		String canonicalEntryPath = file.getCanonicalPath();
-		Assert.state(canonicalEntryPath.startsWith(canonicalOutputPath),
+		Path canonicalOutputPath = directory.getCanonicalFile().toPath();
+		Path canonicalEntryPath = file.getCanonicalFile().toPath();
+		Assert.state(isFileContainedInDirectory(canonicalOutputPath, canonicalEntryPath),
 				() -> "Entry '%s' would be written to '%s'. This is outside the output location of '%s'. Verify the contents of your archive."
 					.formatted(name, canonicalEntryPath, canonicalOutputPath));
 		return file;
 	}
 
+	private static boolean isFileContainedInDirectory(Path directory, Path file) {
+		return !file.equals(directory) && file.startsWith(directory);
+	}
+
 	@FunctionalInterface
 	private interface EntryNameTransformer {
 
@@ -515,9 +521,9 @@ class ExtractCommand extends Command {
 		}
 
 		private File assertLayerDirectoryLocation(File layerDirectory, String layerName) throws IOException {
-			String canonicalOutputPath = this.directory.getCanonicalPath() + File.separator;
-			String canonicalLayerPath = layerDirectory.getCanonicalPath();
-			Assert.state(canonicalLayerPath.startsWith(canonicalOutputPath),
+			Path canonicalOutputPath = this.directory.getCanonicalFile().toPath();
+			Path canonicalLayerPath = layerDirectory.getCanonicalFile().toPath();
+			Assert.state(isFileContainedInDirectory(canonicalOutputPath, canonicalLayerPath),
 					() -> "Layer '%s' would be written to '%s'. This is outside the output location of '%s'. Verify the contents of your archive."
 						.formatted(layerName, canonicalLayerPath, canonicalOutputPath));
 			return layerDirectory;
diff --git a/loader/spring-boot-jarmode-tools/src/test/java/org/springframework/boot/jarmode/tools/ExtractCommandTests.java b/loader/spring-boot-jarmode-tools/src/test/java/org/springframework/boot/jarmode/tools/ExtractCommandTests.java
index 2f25c094d1a..911318f9e69 100644
--- a/loader/spring-boot-jarmode-tools/src/test/java/org/springframework/boot/jarmode/tools/ExtractCommandTests.java
+++ b/loader/spring-boot-jarmode-tools/src/test/java/org/springframework/boot/jarmode/tools/ExtractCommandTests.java
@@ -20,11 +20,13 @@ import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.nio.file.attribute.BasicFileAttributeView;
 import java.nio.file.attribute.BasicFileAttributes;
 import java.time.Instant;
 import java.time.temporal.ChronoUnit;
 import java.util.Enumeration;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.jar.Manifest;
@@ -45,6 +47,7 @@ import static org.assertj.core.api.Assertions.assertThatIllegalStateException;
  * Tests for {@link ExtractCommand}.
  *
  * @author Moritz Halbritter
+ * @author Dongliang Xie
  */
 class ExtractCommandTests extends AbstractJarModeTests {
 
@@ -370,6 +373,38 @@ class ExtractCommandTests extends AbstractJarModeTests {
 				.doesNotContain("test/spring-boot-loader/org/springframework/boot/loader/launch/JarLauncher.class");
 		}
 
+		@Test
+		void extractWhenDestinationIsFileSystemRoot() throws IOException {
+			Path layerDirectory = ExtractCommandTests.this.tempDir.toPath()
+				.resolve("root-output")
+				.resolve("dependencies")
+				.toAbsolutePath()
+				.normalize();
+			Path outputRoot = layerDirectory.getRoot();
+			String layerName = outputRoot.relativize(layerDirectory).toString().replace(File.separatorChar, '/');
+			Layers layers = new Layers() {
+
+				@Override
+				public Iterator<String> iterator() {
+					return List.of(layerName).iterator();
+				}
+
+				@Override
+				public String getLayer(String entryName) {
+					return layerName;
+				}
+
+				@Override
+				public String getApplicationLayerName() {
+					return layerName;
+				}
+
+			};
+			runCommand((context) -> new ExtractCommand(context, layers), ExtractCommandTests.this.archive,
+					"--destination", outputRoot.toString(), "--force", "--launcher", "--layers");
+			assertThat(layerDirectory.resolve("BOOT-INF/lib/dependency-1.jar")).exists();
+		}
+
 	}
 
 }