diff --git a/gnu/local.mk b/gnu/local.mk
index b7e19b6bc2..2ed70c98bf 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1489,6 +1489,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/lierolibre-newer-libconfig.patch		\
   %D%/packages/patches/lierolibre-remove-arch-warning.patch	\
   %D%/packages/patches/lierolibre-try-building-other-arch.patch	\
+  %D%/packages/patches/lightgbm-use-system-libraries.patch	\
   %D%/packages/patches/linbox-fix-pkgconfig.patch		\
   %D%/packages/patches/linphone-desktop-without-sdk.patch	\
   %D%/packages/patches/linux-libre-infodocs-target.patch	\
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 37d4ef78ad..248e318eea 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -83,9 +83,11 @@ (define-module (gnu packages machine-learning)
   #:use-module (gnu packages ninja)
   #:use-module (gnu packages ocaml)
   #:use-module (gnu packages onc-rpc)
+  #:use-module (gnu packages opencl)
   #:use-module (gnu packages parallel)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
@@ -1472,31 +1474,27 @@ (define-public python-autograd
 (define-public lightgbm
   (package
     (name "lightgbm")
-    (version "2.0.12")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/Microsoft/LightGBM")
-                     (commit (string-append "v" version))))
-              (sha256
-               (base32
-                "0jlvyn7k81dzrh9ij3zw576wbgiwmmr26rzpdxjn1dbpc3njpvzi"))
-              (file-name (git-file-name name version))))
-    (native-inputs
-     (list python-pytest python-nose))
-    (inputs
-     (list openmpi))
-    (propagated-inputs
-     (list python-numpy python-scipy))
+    (version "3.3.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Microsoft/LightGBM")
+             (commit (string-append "v" version))))
+       (patches
+        (search-patches "lightgbm-use-system-libraries.patch"))
+       (sha256
+        (base32 "0fljcnlj02pn2y5lxq16rsg6hm0wq4adzrl52i0s8whpcdrgsc0a"))
+       (file-name (git-file-name name version))))
     (arguments
-     `(#:configure-flags
-       '("-DUSE_MPI=ON")
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (with-directory-excursion "../source"
-               (invoke "pytest" "tests/c_api_test/test_.py")))))))
+     (list
+      #:tests? #f        ; FIXME: googletest is not found by CMake
+      #:test-target "testlightgbm"
+      #:configure-flags #~(list "-DBUILD_CPP_TEST=OFF"
+                                "-DUSE_GPU=ON" ;using OpenCL
+                                "-DUSE_MPI=ON")))
+    (native-inputs (list opencl-headers))
+    (inputs (list boost eigen fast-double-parser fmt ocl-icd openmpi))
     (build-system cmake-build-system)
     (home-page "https://github.com/Microsoft/LightGBM")
     (synopsis "Gradient boosting framework based on decision tree algorithms")
diff --git a/gnu/packages/patches/lightgbm-use-system-libraries.patch b/gnu/packages/patches/lightgbm-use-system-libraries.patch
new file mode 100644
index 0000000000..115ca02775
--- /dev/null
+++ b/gnu/packages/patches/lightgbm-use-system-libraries.patch
@@ -0,0 +1,58 @@
+From 894648291b9629d51785e4fd1cae820d2858e039 Mon Sep 17 00:00:00 2001
+From: Vinicius Monego <monego@posteo.net>
+Date: Mon, 31 May 2021 21:23:52 -0300
+Subject: [PATCH] Use system libraries.
+
+---
+ CMakeLists.txt                  | 11 ++++++++---
+ include/LightGBM/utils/common.h |  4 ++--
+ 2 files changed, 10 insertions(+), 5 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index b845f36..560e477 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -93,9 +93,6 @@ if(USE_SWIG)
+   endif()
+ endif(USE_SWIG)
+ 
+-SET(EIGEN_DIR "${PROJECT_SOURCE_DIR}/external_libs/eigen")
+-include_directories(${EIGEN_DIR})
+-
+ # See https://gitlab.com/libeigen/eigen/-/blob/master/COPYING.README
+ ADD_DEFINITIONS(-DEIGEN_MPL2_ONLY)
+ 
+@@ -399,6 +396,14 @@ if(USE_SWIG)
+   endif()
+ endif(USE_SWIG)
+ 
++find_package (Eigen3 3.3 REQUIRED NO_MODULE)
++TARGET_LINK_LIBRARIES (lightgbm Eigen3::Eigen)
++TARGET_LINK_LIBRARIES (_lightgbm Eigen3::Eigen)
++
++find_package(fmt)
++TARGET_LINK_LIBRARIES(lightgbm fmt::fmt)
++TARGET_LINK_LIBRARIES(_lightgbm fmt::fmt)
++
+ if(USE_MPI)
+   TARGET_LINK_LIBRARIES(lightgbm ${MPI_CXX_LIBRARIES})
+   TARGET_LINK_LIBRARIES(_lightgbm ${MPI_CXX_LIBRARIES})
+diff --git a/include/LightGBM/utils/common.h b/include/LightGBM/utils/common.h
+index 4357357..00101a5 100644
+--- a/include/LightGBM/utils/common.h
++++ b/include/LightGBM/utils/common.h
+@@ -32,9 +32,9 @@
+ 
+ #if (!((defined(sun) || defined(__sun)) && (defined(__SVR4) || defined(__svr4__))))
+ #define FMT_HEADER_ONLY
+-#include "../../../external_libs/fmt/include/fmt/format.h"
++#include "fmt/format.h"
+ #endif
+-#include "../../../external_libs/fast_double_parser/include/fast_double_parser.h"
++#include "fast_double_parser.h"
+ 
+ #ifdef _MSC_VER
+ #include <intrin.h>
+-- 
+2.31.1
+
