diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/JarWriter.java b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/JarWriter.java
index caedb7fffc9..2316552991d 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/JarWriter.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/JarWriter.java
@@ -134,7 +134,7 @@ public class JarWriter implements LoaderClassesWriter, AutoCloseable {
 		Enumeration<JarEntry> entries = jarFile.entries();
 		while (entries.hasMoreElements()) {
 			JarArchiveEntry entry = new JarArchiveEntry(entries.nextElement());
-			setUpStoredEntryIfNecessary(jarFile, entry);
+			setUpEntry(jarFile, entry);
 			try (ZipHeaderPeekInputStream inputStream = new ZipHeaderPeekInputStream(
 					jarFile.getInputStream(entry))) {
 				EntryWriter entryWriter = new InputStreamEntryWriter(inputStream, true);
@@ -146,13 +146,15 @@ public class JarWriter implements LoaderClassesWriter, AutoCloseable {
 		}
 	}
 
-	private void setUpStoredEntryIfNecessary(JarFile jarFile, JarArchiveEntry entry)
-			throws IOException {
+	private void setUpEntry(JarFile jarFile, JarArchiveEntry entry) throws IOException {
 		try (ZipHeaderPeekInputStream inputStream = new ZipHeaderPeekInputStream(
 				jarFile.getInputStream(entry))) {
 			if (inputStream.hasZipHeader() && entry.getMethod() != ZipEntry.STORED) {
 				new CrcAndSize(inputStream).setupStoredEntry(entry);
 			}
+			else {
+				entry.setCompressedSize(-1);
+			}
 		}
 	}
 
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
index b8416d00880..be35e8bb9b3 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
@@ -18,6 +18,7 @@ package org.springframework.boot.loader.tools;
 
 import java.io.ByteArrayInputStream;
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.attribute.PosixFilePermission;
@@ -25,11 +26,14 @@ import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.Enumeration;
 import java.util.List;
+import java.util.Random;
 import java.util.jar.Attributes;
 import java.util.jar.JarEntry;
 import java.util.jar.JarFile;
 import java.util.jar.Manifest;
+import java.util.zip.Deflater;
 import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
 
 import org.apache.commons.compress.archivers.zip.ZipArchiveEntry;
 import org.apache.commons.compress.archivers.zip.ZipFile;
@@ -638,6 +642,28 @@ public class RepackagerTests {
 				"META-INF/MANIFEST.MF", "a/", "a/b/", "a/b/C.class");
 	}
 
+	@Test
+	public void jarThatUsesCustomCompressionConfigurationCanBeRepackaged()
+			throws IOException {
+		File source = this.temporaryFolder.newFile("source.jar");
+		ZipOutputStream output = new ZipOutputStream(new FileOutputStream(source)) {
+			{
+				this.def = new Deflater(Deflater.NO_COMPRESSION, true);
+			}
+		};
+		byte[] data = new byte[1024 * 1024];
+		new Random().nextBytes(data);
+		ZipEntry entry = new ZipEntry("entry.dat");
+		output.putNextEntry(entry);
+		output.write(data);
+		output.closeEntry();
+		output.close();
+		File dest = this.temporaryFolder.newFile("dest.jar");
+		Repackager repackager = new Repackager(source);
+		repackager.setMainClass("com.example.Main");
+		repackager.repackage(dest, NO_LIBRARIES);
+	}
+
 	private File createLibrary() throws IOException {
 		TestJarFile library = new TestJarFile(this.temporaryFolder);
 		library.addClass("com/example/library/Library.class",