Objective To compare the safety and effectiveness of endoscopic full‑thickness resection (EFR) and cap‑assisted endoscopic full‑thickness resection (EFR‑C) in the treatment of small gastric stromal tumors (≤1.5 cm) in the elderly (≥60 years old). Methods Data of elderly patients with small gastric stromal tumors who received EFR (41 cases) or EFR‑C (25 cases) at Nanjing Drum Tower Hospital from May 2012 to August 2020 were analyzed retrospectively. The clinicopathological characteristics, the procedures, intraoperative and postoperative complications, postoperative efficacy and economic benefits were compared between the two groups. Results The R0 resection rates of the EFR group and the EFR‑C group were 95.1% (39/41) and 100% (25/25), respectively. The operation time [45.0 (32.5, 66.5) min VS 30.0 (20.0, 42.5) min, U=259.500, P=0.001] and resection time [30.0 (20.0, 50.5) min VS 9.0 (6.5, 16.5) min, U=127.000, P<0.001] of the EFR group were significantly longer than those of the EFR‑C group. The rate of hot clamp use in the EFR group was higher than that in the EFR‑C group [75.6% (31/41) VS 12.0% (3/25), χ２=25.159, P<0.001]. The postoperative white blood cell count [8.3 (6.6,10.4)×109/L VS 6.3 (5.0,7.7) ×109/L,U=271.000, P=0.001] and postoperative neutrophil percentage (77.6%±8.8% VS 73.0%±6.8%, t=2.256, P=0.027) in the EFR group were higher than those in the EFR‑C group. The postoperative antibiotic day in the EFR group was longer than that in the EFR‑C group (2.8±2.0 days VS 1.0±2.0 days, t=3.625, P=0.001). The hospitalization costs in the EFR group were significantly higher than those in the EFR‑C group (20 595.0±3 653.3 yuan VS 13 209.0±4 458.9 yuan, t=7.323, P<0.001). There was no recurrence or metastasis during the follow‑up period. Conclusion EFR and EFR‑C are safe and effective for the treatment of small gastric stromal tumors in the elderly. Compared with EFR, EFR‑C needs shorter operation time and lower medical costs, yields less postoperative inflammation, and is more suitable for the treatment of small gastric stromal tumors in the elderly.