Data of 55 cases of gastric neuroendocrine neoplasms (G-NENS) with diameter ≤12 mm in the First Affiliated Hospital of Zhengzhou University from August 2014 to August 2019 were retrospectively analyzed. According to the methods of endoscopic resection, the patients were divided into two groups: the endoscopic mucosal resection with a cap (EMR-C) group (35 cases) and the endoscopic submucosal dissection (ESD) group (20 cases). The results showed that the success rates of operation, the whole resection rates and the complete resection rates were all 100.0% in the two groups. Compared with the ESD group, the EMR-C group had a shorter median operation time (12.00 min VS 28.35 min, P<0.001), less mean hospitalization costs (21 165.19 yuan VS 28 400.35 yuan, P=0.004), and a similar overall incidence of complications [2.86% (1/35) VS 0, P=1.000]. By March 2020, the recurrence rate of EMR-C group and ESD group were 28.6% (10/35) and 15.0% (3/20), respectively, without significant difference (P=0.418). It is suggested that for G-NENS with diameter ≤12 mm, without muscular invasion, lymph node metastasis or distant metastasis, EMR-C and ESD are both safe and effective, but EMR-C has more advantages in terms of operation time and hospitalization costs.