diff --git a/.ci/test_r_package_valgrind.sh b/.ci/test_r_package_valgrind.sh
index 80a2830b742..fc27689f909 100755
--- a/.ci/test_r_package_valgrind.sh
+++ b/.ci/test_r_package_valgrind.sh
@@ -1,7 +1,9 @@
 #!/bin/bash
 
 RDscriptvalgrind -e "install.packages(c('R6', 'data.table', 'jsonlite', 'Matrix', 'testthat'), repos = 'https://cran.r-project.org', Ncpus = parallel::detectCores())" || exit -1
-sh build-cran-package.sh || exit -1
+sh build-cran-package.sh \
+  --r-executable=RDvalgrind \
+  || exit -1
 RDvalgrind CMD INSTALL --preclean --install-tests lightgbm_*.tar.gz || exit -1
 
 cd R-package/tests
diff --git a/.github/workflows/r_package.yml b/.github/workflows/r_package.yml
index 6f07c6e4f39..13127c25b04 100644
--- a/.github/workflows/r_package.yml
+++ b/.github/workflows/r_package.yml
@@ -195,7 +195,7 @@ jobs:
         shell: bash
         run: |
           RDscript${{ matrix.r_customization }} -e "install.packages(c('R6', 'data.table', 'jsonlite', 'Matrix', 'testthat'), repos = 'https://cran.r-project.org', Ncpus = parallel::detectCores())"
-          sh build-cran-package.sh
+          sh build-cran-package.sh --r-executable=RD${{ matrix.r_customization }}
           RD${{ matrix.r_customization }} CMD INSTALL lightgbm_*.tar.gz || exit -1
       - name: Run tests with sanitizers
         shell: bash
diff --git a/R-package/README.md b/R-package/README.md
index 918db731c48..352071f0ad4 100644
--- a/R-package/README.md
+++ b/R-package/README.md
@@ -394,7 +394,7 @@ RDscript${R_CUSTOMIZATION} \
   -e "install.packages(c('R6', 'data.table', 'jsonlite', 'Matrix', 'testthat'), repos = 'https://cran.r-project.org', Ncpus = parallel::detectCores())"
 
 # install lightgbm
-sh build-cran-package.sh
+sh build-cran-package.sh --r-executable=RD${R_CUSTOMIZATION}
 RD${R_CUSTOMIZATION} \
   CMD INSTALL lightgbm_*.tar.gz
 
@@ -423,7 +423,8 @@ docker run \
 
 RDscriptvalgrind -e "install.packages(c('R6', 'data.table', 'jsonlite', 'Matrix', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
 
-sh build-cran-package.sh
+sh build-cran-package.sh \
+    --r-executable=RDvalgrind
 
 RDvalgrind CMD INSTALL \
     --preclean \
diff --git a/build-cran-package.sh b/build-cran-package.sh
index 967ee4a03c8..e4def4a1465 100755
--- a/build-cran-package.sh
+++ b/build-cran-package.sh
@@ -4,11 +4,40 @@
 #     Prepare a source distribution of the R package
 #     to be submitted to CRAN.
 #
+# [arguments] 
+#
+#     --r-executable Customize the R executable used by `R CMD build`.
+#                    Useful if building the R package in an environment with
+#                    non-standard builds of R, such as those provided in
+#                    https://github.com/wch/r-debug.
+#
 # [usage]
+#
+#     # default usage
 #     sh build-cran-package.sh
+#
+#     # custom R build
+#     sh build-cran-package.sh --r-executable=RDvalgrind
 
 set -e
 
+LGB_R_EXECUTABLE=R
+
+while [ $# -gt 0 ]; do
+  case "$1" in
+    --r-executable=*)
+      LGB_R_EXECUTABLE="${1#*=}"
+      ;;
+    *)
+      echo "invalid argument '${1}'"
+      exit -1
+      ;;
+  esac
+  shift
+done
+
+echo "Building lightgbm with R executable: ${LGB_R_EXECUTABLE}"
+
 ORIG_WD="$(pwd)"
 TEMP_R_DIR="$(pwd)/lightgbm_r"
 
@@ -140,7 +169,7 @@ cd "${TEMP_R_DIR}"
 
 cd "${ORIG_WD}"
 
-R CMD build \
+"${LGB_R_EXECUTABLE}" CMD build \
     --keep-empty-dirs \
     lightgbm_r