diff --git a/.travis.yml b/.travis.yml
index 8cd6c91c2b509..ab29ec8fdd501 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -360,7 +360,7 @@ matrix:
     - export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$TRAVIS_BUILD_DIR/cpp-install/lib/pkgconfig
     - pushd ${TRAVIS_BUILD_DIR}/r
     after_success:
-    - Rscript -e 'covr::codecov()'
+    - Rscript ../ci/travis_upload_r_coverage.R
 
 
 after_failure:
diff --git a/ci/travis_upload_r_coverage.R b/ci/travis_upload_r_coverage.R
new file mode 100644
index 0000000000000..89c102f0f0330
--- /dev/null
+++ b/ci/travis_upload_r_coverage.R
@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+library(covr)
+# Hack file paths to include the subdirectory
+trace("to_codecov", quote(per_line <- function(x) {
+   out <- covr:::per_line(x)
+   setNames(out, paste0("r/", names(out)))
+ }), where = package_coverage)
+codecov()