diff --git a/perception/BUILD.bazel b/perception/BUILD.bazel
index 0614efd7dcf0..f99ca6053197 100644
--- a/perception/BUILD.bazel
+++ b/perception/BUILD.bazel
@@ -42,7 +42,7 @@ drake_cc_library(
     deps = [
         "//common:unused",
         "@abseil_cpp_internal//absl/container:flat_hash_map",
-        "@nanoflann",
+        "@nanoflann_internal//:nanoflann",
     ],
 )
 
diff --git a/perception/point_cloud.cc b/perception/point_cloud.cc
index b31823216131..772e421eff24 100644
--- a/perception/point_cloud.cc
+++ b/perception/point_cloud.cc
@@ -6,9 +6,9 @@
 #include <vector>
 
 #include "absl/container/flat_hash_map.h"
+#include <drake_vendor/nanoflann.hpp>
 #include <fmt/format.h>
 #include <fmt/ostream.h>
-#include <nanoflann.hpp>
 
 #include "drake/common/drake_assert.h"
 #include "drake/common/drake_throw.h"
diff --git a/tools/workspace/BUILD.bazel b/tools/workspace/BUILD.bazel
index 14fcbb8557e0..a96587beadc2 100644
--- a/tools/workspace/BUILD.bazel
+++ b/tools/workspace/BUILD.bazel
@@ -90,6 +90,7 @@ _DRAKE_EXTERNAL_PACKAGE_INSTALLS = ["@%s//:install" % p for p in [
     "meshcat_python",
     "msgpack_lite_js",
     "net_sf_jchart2d",
+    "nanoflann_internal",
     "nlopt_internal",
     "org_apache_xmlgraphics_commons",
     "petsc",
diff --git a/tools/workspace/default.bzl b/tools/workspace/default.bzl
index 8a3fab06f7b1..98bb3027336f 100644
--- a/tools/workspace/default.bzl
+++ b/tools/workspace/default.bzl
@@ -63,7 +63,7 @@ load("@drake//tools/workspace/msgpack:repository.bzl", "msgpack_repository")
 load("@drake//tools/workspace/msgpack_lite_js:repository.bzl", "msgpack_lite_js_repository")  # noqa
 load("@drake//tools/workspace/mypy_extensions_internal:repository.bzl", "mypy_extensions_internal_repository")  # noqa
 load("@drake//tools/workspace/mypy_internal:repository.bzl", "mypy_internal_repository")  # noqa
-load("@drake//tools/workspace/nanoflann:repository.bzl", "nanoflann_repository")  # noqa
+load("@drake//tools/workspace/nanoflann_internal:repository.bzl", "nanoflann_internal_repository")  # noqa
 load("@drake//tools/workspace/net_sf_jchart2d:repository.bzl", "net_sf_jchart2d_repository")  # noqa
 load("@drake//tools/workspace/nlopt:repository.bzl", "nlopt_repository")
 load("@drake//tools/workspace/nlopt_internal:repository.bzl", "nlopt_internal_repository")  # noqa
@@ -278,8 +278,8 @@ def add_default_repositories(excludes = [], mirrors = DEFAULT_MIRRORS):
         mypy_extensions_internal_repository(name = "mypy_extensions_internal", mirrors = mirrors)  # noqa
     if "mypy_internal" not in excludes:
         mypy_internal_repository(name = "mypy_internal", mirrors = mirrors)
-    if "nanoflann" not in excludes:
-        nanoflann_repository(name = "nanoflann", mirrors = mirrors)
+    if "nanoflann_internal" not in excludes:
+        nanoflann_internal_repository(name = "nanoflann_internal", mirrors = mirrors)  # noqa
     if "net_sf_jchart2d" not in excludes:
         net_sf_jchart2d_repository(name = "net_sf_jchart2d", mirrors = mirrors)
     if "nlopt" not in excludes:
diff --git a/tools/workspace/nanoflann/BUILD.bazel b/tools/workspace/nanoflann_internal/BUILD.bazel
similarity index 100%
rename from tools/workspace/nanoflann/BUILD.bazel
rename to tools/workspace/nanoflann_internal/BUILD.bazel
diff --git a/tools/workspace/nanoflann/package.BUILD.bazel b/tools/workspace/nanoflann_internal/package.BUILD.bazel
similarity index 82%
rename from tools/workspace/nanoflann/package.BUILD.bazel
rename to tools/workspace/nanoflann_internal/package.BUILD.bazel
index 3f98490cb4f0..5d7b8eca81ef 100644
--- a/tools/workspace/nanoflann/package.BUILD.bazel
+++ b/tools/workspace/nanoflann_internal/package.BUILD.bazel
@@ -12,8 +12,8 @@ package(default_visibility = ["//visibility:public"])
 cc_library(
     name = "nanoflann",
     hdrs = ["include/nanoflann.hpp"],
-    includes = ["include"],
-    deps = [],
+    include_prefix = "drake_vendor",
+    strip_include_prefix = "include",
     linkstatic = 1,
 )
 
diff --git a/tools/workspace/nanoflann_internal/patches/namespace.patch b/tools/workspace/nanoflann_internal/patches/namespace.patch
new file mode 100644
index 000000000000..f471a526d45f
--- /dev/null
+++ b/tools/workspace/nanoflann_internal/patches/namespace.patch
@@ -0,0 +1,21 @@
+Add a drake_vendor namespace ala tools/workspace/vendor_cxx
+
+This prevents link-time symbol conflicts in case code downstream of
+Drake wants to use a different build of nanoflann.
+
+--- include/nanoflann.hpp.orig
++++ include/nanoflann.hpp
+@@ -70,6 +70,7 @@
+ #endif
+ #endif
+ 
++inline namespace drake_vendor __attribute__ ((visibility ("hidden"))) {
+ namespace nanoflann
+ {
+ /** @addtogroup nanoflann_grp nanoflann C++ library for ANN
+@@ -2414,3 +2415,4 @@
+ 
+ /** @} */  // end of grouping
+ }  // namespace nanoflann
++}  // namespace drake_vendor
+\ No newline at end of file
diff --git a/tools/workspace/nanoflann/repository.bzl b/tools/workspace/nanoflann_internal/repository.bzl
similarity index 79%
rename from tools/workspace/nanoflann/repository.bzl
rename to tools/workspace/nanoflann_internal/repository.bzl
index 96f3ada3ea11..c7ec1f138668 100644
--- a/tools/workspace/nanoflann/repository.bzl
+++ b/tools/workspace/nanoflann_internal/repository.bzl
@@ -2,7 +2,7 @@
 
 load("@drake//tools/workspace:github.bzl", "github_archive")
 
-def nanoflann_repository(
+def nanoflann_internal_repository(
         name,
         mirrors = None):
     github_archive(
@@ -11,5 +11,8 @@ def nanoflann_repository(
         commit = "v1.4.3",
         sha256 = "cbcecf22bec528a8673a113ee9b0e134f91f1f96be57e913fa1f74e98e4449fa",  # noqa
         build_file = ":package.BUILD.bazel",
+        patches = [
+            ":patches/namespace.patch",
+        ],
         mirrors = mirrors,
     )