diff --git a/core/src/main/java/org/apache/druid/data/input/impl/LocalInputSource.java b/core/src/main/java/org/apache/druid/data/input/impl/LocalInputSource.java
index e811de7cc30..4a3dd9e257d 100644
--- a/core/src/main/java/org/apache/druid/data/input/impl/LocalInputSource.java
+++ b/core/src/main/java/org/apache/druid/data/input/impl/LocalInputSource.java
@@ -87,13 +87,28 @@ public class LocalInputSource extends AbstractInputSource implements SplittableI
   }
 
   @Nullable
-  @JsonProperty
-  @JsonInclude(JsonInclude.Include.NON_NULL)
   public File getBaseDir()
   {
     return baseDir;
   }
 
+  /**
+   * Returns the base directory for serialization. This is better than returning {@link File} directly, because
+   * Jackson serializes {@link File} using {@link File#getAbsolutePath()}, and we'd prefer to not force relative
+   * path resolution as part of serialization.
+   */
+  @Nullable
+  @JsonProperty("baseDir")
+  @JsonInclude(JsonInclude.Include.NON_NULL)
+  private String getBaseDirForSerialization()
+  {
+    if (baseDir == null) {
+      return null;
+    } else {
+      return baseDir.getPath();
+    }
+  }
+
   @Nullable
   @JsonProperty
   @JsonInclude(JsonInclude.Include.NON_NULL)
@@ -102,13 +117,23 @@ public class LocalInputSource extends AbstractInputSource implements SplittableI
     return filter;
   }
 
-  @JsonProperty
-  @JsonInclude(JsonInclude.Include.NON_EMPTY)
   public List<File> getFiles()
   {
     return files;
   }
 
+  /**
+   * Returns the list of file paths for serialization. This is better than returning {@link File} directly, because
+   * Jackson serializes {@link File} using {@link File#getAbsolutePath()}, and we'd prefer to not force relative
+   * path resolution as part of serialization.
+   */
+  @JsonProperty("files")
+  @JsonInclude(JsonInclude.Include.NON_EMPTY)
+  private List<String> getFilesForSerialization()
+  {
+    return getFiles().stream().map(File::getPath).collect(Collectors.toList());
+  }
+
   @Override
   public Stream<InputSplit<List<File>>> createSplits(InputFormat inputFormat, @Nullable SplitHintSpec splitHintSpec)
   {
@@ -233,9 +258,9 @@ public class LocalInputSource extends AbstractInputSource implements SplittableI
   public String toString()
   {
     return "LocalInputSource{" +
-        "baseDir=\"" + baseDir +
-        "\", filter=" + filter +
-        ", files=" + files +
-        "}";
+           "baseDir=\"" + baseDir +
+           "\", filter=" + filter +
+           ", files=" + files +
+           "}";
   }
 }
diff --git a/core/src/test/java/org/apache/druid/data/input/impl/LocalInputSourceTest.java b/core/src/test/java/org/apache/druid/data/input/impl/LocalInputSourceTest.java
index 67361b8171b..2917a2aa5f2 100644
--- a/core/src/test/java/org/apache/druid/data/input/impl/LocalInputSourceTest.java
+++ b/core/src/test/java/org/apache/druid/data/input/impl/LocalInputSourceTest.java
@@ -20,6 +20,7 @@
 package org.apache.druid.data.input.impl;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Lists;
 import nl.jqno.equalsverifier.EqualsVerifier;
 import org.apache.druid.data.input.InputSource;
@@ -51,7 +52,7 @@ public class LocalInputSourceTest
   public TemporaryFolder temporaryFolder = new TemporaryFolder();
 
   @Test
-  public void testSerde() throws IOException
+  public void testSerdeAbsoluteBaseDir() throws IOException
   {
     final ObjectMapper mapper = new ObjectMapper();
     final LocalInputSource source = new LocalInputSource(new File("myFile").getAbsoluteFile(), "myFilter");
@@ -60,6 +61,33 @@ public class LocalInputSourceTest
     Assert.assertEquals(source, fromJson);
   }
 
+  @Test
+  public void testSerdeRelativeBaseDir() throws IOException
+  {
+    final ObjectMapper mapper = new ObjectMapper();
+    final LocalInputSource source = new LocalInputSource(new File("myFile"), "myFilter");
+    final byte[] json = mapper.writeValueAsBytes(source);
+    final LocalInputSource fromJson = (LocalInputSource) mapper.readValue(json, InputSource.class);
+    Assert.assertEquals(source, fromJson);
+  }
+
+  @Test
+  public void testSerdeMixedAbsoluteAndRelativeFiles() throws IOException
+  {
+    final ObjectMapper mapper = new ObjectMapper();
+    final LocalInputSource source = new LocalInputSource(
+        null,
+        null,
+        ImmutableList.of(
+            new File("myFile1"),
+            new File("myFile2").getAbsoluteFile()
+        )
+    );
+    final byte[] json = mapper.writeValueAsBytes(source);
+    final LocalInputSource fromJson = (LocalInputSource) mapper.readValue(json, InputSource.class);
+    Assert.assertEquals(source, fromJson);
+  }
+
   @Test
   public void testEquals()
   {
diff --git a/docs/multi-stage-query/reference.md b/docs/multi-stage-query/reference.md
index 5016b6ab484..1768572e423 100644
--- a/docs/multi-stage-query/reference.md
+++ b/docs/multi-stage-query/reference.md
@@ -134,10 +134,6 @@ You must either provide the `baseDir` or the list of `files`. You can provide bo
 the files are assumed relative to the `baseDir`. If you provide a `filter`, you must provide the
 `baseDir`.
 
-Note that, due to [Issue #13359](https://github.com/apache/druid/issues/13359), the functionality
-described above is broken. Until that issue is resolved, you must provide one or more absolute
-file paths in the `files` property and the other two properties are unavailable.
-
 #### Table Function Format
 
 Each of the table functions above requires that you specify a format.