We introduce a graphics processing unit (GPU) acceleration to reconstructing holograms of phase retrieval holography for a drastic reduction of the execution time. We conducted GPU acceleration using the FFT library CUFFT on the GPU chip (GEFORCE GTX 1050, GDDR5 2GB, NVIDIA). We also used Intel Xeon CPU (E5-2690, 2.90GHz, Intel), the memory of 24 GB, and the operating system of Ubuntu 16.04 to compare GPU and CPU. Reconstructed volumes changed from 2562 × 128 voxels to 20482 × 1024 voxel to compare execution times. The ratio of the time of GPU to that of CPUs is constantly higher than 100 times except for small volume. We also demonstrated that GPU acceleration decreased the time by observing falling particles, recorded in 40 frames, from particle feeder. As a result, it is found that the execution time is reduced from 13 hours to 30 minutes.