--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -177,7 +177,13 @@
 if (OCTOPUS_CUDA)
 	find_package(CUDAToolkit)
 	set(HAVE_CUDA 1)
-	set(HAVE_NVTX 1)
+	# NVTX profiling relies on the legacy nvToolsExt library, which NVIDIA dropped
+	# from the redistributable cuda_nvtx package in CUDA 12.9. Enable profiling
+	# only when the legacy target is available (CUDA < 12.9); on 12.9+ nvtx_low.cc
+	# falls back to no-op markers (and links the header-only nvtx3 target).
+	if (TARGET CUDA::nvToolsExt)
+		set(HAVE_NVTX 1)
+	endif ()
 	set_package_properties(CUDAToolkit PROPERTIES TYPE REQUIRED)
 	if (OCTOPUS_MPI)
 		include(cmake/GPUawareMPI.cmake)
--- a/src/basic/CMakeLists.txt
+++ b/src/basic/CMakeLists.txt
@@ -90,8 +90,14 @@
 		CUDA::cuda_driver
 		CUDA::cublas
 		CUDA::cufft
-		CUDA::nvrtc
-		CUDA::nvToolsExt)
+		CUDA::nvrtc)
+	# Legacy nvToolsExt (shared lib) was dropped from cuda_nvtx in CUDA 12.9.
+	# Link it when present; otherwise fall back to the header-only nvtx3.
+	if (TARGET CUDA::nvToolsExt)
+		target_link_libraries(Octopus_lib PRIVATE CUDA::nvToolsExt)
+	elseif (TARGET CUDA::nvtx3)
+		target_link_libraries(Octopus_lib PRIVATE CUDA::nvtx3)
+	endif ()
 endif ()
 
 if (OCTOPUS_HIP)