diff --git a/sphinxdocs/sphinxdocs/private/sphinx.bzl b/sphinxdocs/sphinxdocs/private/sphinx.bzl
index c42b42ebc6..24c5e9f9d1 100644
--- a/sphinxdocs/sphinxdocs/private/sphinx.bzl
+++ b/sphinxdocs/sphinxdocs/private/sphinx.bzl
@@ -100,7 +100,7 @@ def sphinx_docs(
         sphinx,
         config,
         formats,
-        strip_prefix = "",
+        strip_prefix = None,
         extra_opts = [],
         tools = [],
         allow_persistent_workers = True,
@@ -133,10 +133,10 @@ def sphinx_docs(
         config: {type}`label` the Sphinx config file (`conf.py`) to use.
         formats: (list of str) the formats (`-b` flag) to generate documentation
             in. Each format will become an output group.
-        strip_prefix: {type}`str` A prefix to remove from the file paths of the
-            source files. e.g., given `//sphinxdocs/docs:foo.md`, stripping `docs/` makes
-            Sphinx see `foo.md` in its generated source directory. If not
-            specified, then {any}`native.package_name` is used.
+        strip_prefix: {type}`str | None` A prefix to remove from the file paths of the
+            source files. An empty string (`""`) means no prefix stripping; `None`
+            means {any}`native.package_name` is used. e.g., given `//docs:foo.md`,
+            stripping `docs/` makes Sphinx see `foo.md` in its generated source directory.
         extra_opts: {type}`list[str]` Additional options to pass onto Sphinx building.
             On each provided option, a location expansion is performed.
             See {any}`ctx.expand_location`.
@@ -148,6 +148,7 @@ def sphinx_docs(
             This can improve incremental building of docs.
         **kwargs: {type}`dict` Common attributes to pass onto rules.
     """
+    strip_prefix = strip_prefix if strip_prefix != None else native.package_name()
     add_tag(kwargs, "//sphinxdocs:sphinx_docs")
     common_kwargs = copy_propagating_kwargs(kwargs)
 
@@ -355,7 +356,9 @@ def _sphinx_source_tree_impl(ctx):
     # Materialize a file under the `_sources` dir
     def _relocate(source_file, dest_path = None):
         if not dest_path:
-            dest_path = source_file.short_path.removeprefix(ctx.attr.strip_prefix)
+            # Strip leading slash if strip_prefix lacks a trailing slash,
+            # preventing paths.join from treating it as an absolute root.
+            dest_path = source_file.short_path.removeprefix(ctx.attr.strip_prefix).lstrip("/")
 
         dest_path = paths.join(source_prefix, dest_path)
         if source_file.is_directory:
@@ -378,7 +381,9 @@ 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)
+    # Sphinx requires the configuration file to be named conf.py:
+    # https://www.sphinx-doc.org/en/master/usage/configuration.html#module-conf
+    source_conf_file = _relocate(ctx.file.config, "conf.py")
     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"]