diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/zip/ZipCentralDirectoryFileHeaderRecord.java b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/zip/ZipCentralDirectoryFileHeaderRecord.java
index a9ca0a54ad8..673620f155b 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/zip/ZipCentralDirectoryFileHeaderRecord.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/zip/ZipCentralDirectoryFileHeaderRecord.java
@@ -97,8 +97,8 @@ record ZipCentralDirectoryFileHeaderRecord(short versionMadeBy, short versionNee
 			dataBlock.readFully(buffer, extraPos);
 			zipEntry.setExtra(buffer.array());
 		}
-		if ((fileCommentLength() & 0xFFFF) > 0) {
-			long commentPos = MINIMUM_SIZE + fileNameLength + extraLength;
+		if (commentLength > 0) {
+			long commentPos = pos + MINIMUM_SIZE + fileNameLength + extraLength;
 			zipEntry.setComment(ZipString.readString(dataBlock, commentPos, commentLength));
 		}
 	}
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/jar/NestedJarFileTests.java b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/jar/NestedJarFileTests.java
index ac6da2187b8..782dd1369ac 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/jar/NestedJarFileTests.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/jar/NestedJarFileTests.java
@@ -23,10 +23,15 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.lang.ref.Cleaner.Cleanable;
 import java.nio.charset.Charset;
+import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.List;
+import java.util.UUID;
 import java.util.jar.JarEntry;
 import java.util.jar.JarFile;
+import java.util.jar.JarOutputStream;
 import java.util.jar.Manifest;
+import java.util.zip.ZipEntry;
 import java.util.zip.ZipFile;
 
 import org.assertj.core.extractor.Extractors;
@@ -386,4 +391,42 @@ class NestedJarFileTests {
 		}
 	}
 
+	@Test // gh-39166
+	void getCommentAlignsWithJdkJar() throws Exception {
+		File file = new File(this.tempDir, "testcomments.jar");
+		try (JarOutputStream jar = new JarOutputStream(new FileOutputStream(file))) {
+			jar.putNextEntry(new ZipEntry("BOOT-INF/"));
+			jar.closeEntry();
+			jar.putNextEntry(new ZipEntry("BOOT-INF/classes/"));
+			jar.closeEntry();
+			for (int i = 0; i < 5; i++) {
+				ZipEntry entry = new ZipEntry("BOOT-INF/classes/T" + i + ".class");
+				entry.setComment("T" + i);
+				jar.putNextEntry(entry);
+				jar.write(UUID.randomUUID().toString().getBytes());
+				jar.closeEntry();
+			}
+		}
+		List<String> jdk = collectComments(new JarFile(file));
+		List<String> nested = collectComments(new NestedJarFile(file, "BOOT-INF/classes/"));
+		assertThat(nested).isEqualTo(jdk);
+	}
+
+	private List<String> collectComments(JarFile jarFile) throws IOException {
+		try {
+			List<String> comments = new ArrayList<>();
+			Enumeration<JarEntry> entries = jarFile.entries();
+			while (entries.hasMoreElements()) {
+				String comment = entries.nextElement().getComment();
+				if (comment != null) {
+					comments.add(comment);
+				}
+			}
+			return comments;
+		}
+		finally {
+			jarFile.close();
+		}
+	}
+
 }