In order to improve the computational efficiency of synthetic aperture imaging algorithm in the medical endoscopic ultrasound system, the synthetic aperture imaging approach with parallel implementation on graphics processing unit (GPU) is proposed. Firstly, the basic principle and image reconstruction process of synthetic aperture algorithm are introduced. Then, the algorithm is analyzed in parallel processing. Finally, synthetic aperture imaging algorithm for endoscopic ultrasound based on GPU is implemented by using the flexible architecture of single instruction multiple threads (SIMT) of compute unified device architecture (CUDA) programming mode. Multiple simulation experiments of scattering points imaging are compared and analyzed, and the imaging experiment verifications of iron wire, cyst prosthesis and pigskin tissue are carried out by using a self-built endoscopic ultrasound experimental system. The experimental results show that the proposed method can greatly improve the computational efficiency while keeping the same imaging quality and results. When the calculated data size is 1.47 GB (5305×581×64×8 byte), the maximum speedup ratio reaches 50.93.