diff --git a/sphinxdocs/sphinxdocs/private/sphinx.bzl b/sphinxdocs/sphinxdocs/private/sphinx.bzl
index b7c051a154..ea4c5e4501 100644
--- a/sphinxdocs/sphinxdocs/private/sphinx.bzl
+++ b/sphinxdocs/sphinxdocs/private/sphinx.bzl
@@ -373,7 +373,7 @@ def _sphinx_source_tree_impl(ctx):
     # Though Sphinx has a -c flag, we move the config file into the sources
     # directory to make the config more intuitive because some configuration
     # options are relative to the config location, not the sources directory.
-    source_conf_file = _relocate(ctx.file.config)
+    source_conf_file = _relocate(ctx.file.config, paths.basename(ctx.file.config.path))
     sphinx_source_dir_path = paths.dirname(source_conf_file.path)
 
     for src in ctx.attr.srcs:
diff --git a/sphinxdocs/tests/sphinx_docs_conf_in_other_dir/BUILD.bazel b/sphinxdocs/tests/sphinx_docs_conf_in_other_dir/BUILD.bazel
new file mode 100644
index 0000000000..eecbb90897
--- /dev/null
+++ b/sphinxdocs/tests/sphinx_docs_conf_in_other_dir/BUILD.bazel
@@ -0,0 +1,38 @@
+load("@bazel_skylib//rules:build_test.bzl", "build_test")
+load("//sphinxdocs:sphinx.bzl", "sphinx_build_binary", "sphinx_docs")
+
+_TARGET_COMPATIBLE_WITH = select({
+    "@platforms//os:linux": [],
+    "@platforms//os:macos": [],
+    "//conditions:default": ["@platforms//:incompatible"],
+})
+
+genrule(
+    name = "gen_conf",
+    srcs = ["src_conf.py"],
+    outs = ["other_dir/conf.py"],
+    cmd = "cp $(location src_conf.py) $@",
+)
+
+sphinx_docs(
+    name = "docs",
+    srcs = ["index.md"],
+    config = ":gen_conf",
+    formats = ["html"],
+    sphinx = ":sphinx-build",
+    target_compatible_with = _TARGET_COMPATIBLE_WITH,
+)
+
+sphinx_build_binary(
+    name = "sphinx-build",
+    tags = ["manual"],
+    deps = [
+        "@dev_pip//myst_parser",
+        "@dev_pip//sphinx",
+    ],
+)
+
+build_test(
+    name = "docs_build_test",
+    targets = [":docs"],
+)
diff --git a/sphinxdocs/tests/sphinx_docs_conf_in_other_dir/index.md b/sphinxdocs/tests/sphinx_docs_conf_in_other_dir/index.md
new file mode 100644
index 0000000000..cd7d8b4188
--- /dev/null
+++ b/sphinxdocs/tests/sphinx_docs_conf_in_other_dir/index.md
@@ -0,0 +1,3 @@
+# Test Documentation
+
+This is a test document for reproducing conf.py in a separate directory.
diff --git a/sphinxdocs/tests/sphinx_docs_conf_in_other_dir/src_conf.py b/sphinxdocs/tests/sphinx_docs_conf_in_other_dir/src_conf.py
new file mode 100644
index 0000000000..d4f2f45d31
--- /dev/null
+++ b/sphinxdocs/tests/sphinx_docs_conf_in_other_dir/src_conf.py
@@ -0,0 +1,4 @@
+project = "Repro Test"
+copyright = "2026, Test"
+author = "Test"
+extensions = ["myst_parser"]