Chemotherapy is the most commonly used therapeutic method for treating many malignancies including gastric cancer. Due to their non-specific and non-targeted drug delivery, it causes resistance leading to cancer progression, relapse, and metastasis of cancer. To overcome this problem we carried out a study aimed to develop a new cisplatin (Cisp) loaded hydroxyl functionalized single-walled carbon nanotube (OH-SWCNT) nanocarrier system to selectively eliminate gastric cancer stem cells. To our understanding, this is the first study of the non-covalent interaction of cisplatin loaded on the surface of hydroxyl-functionalized single-walled carbon nanotubes by ultrasonication. The physical and morphological characterization was carried out by UV–Vis, FTIR spectroscopy, and TEM. A sustained and controlled release of cisp from OH-SWCNT at all three pHs 3.5, 5.5, and 7.4 was observed. Gastric cancer stem cells were isolated from primary cells and were identified by using CD133+ and CD44+ specific markers. Cisplatin-loaded OH-SWCNT nanocarrier was capable of limiting the self-renewal capacity of both CD133+ and CD44+ populations and also decreasing the number of tumorspheres in gastric CSCs. The cell viability percent of AGS cells was 20% at 250 μg/ml concentration. The IC50 value was less than 50% mol/L at both 200 μg/ml and 250 μg/ml of cisplatin-loaded OH-SWCNT. Our findings suggest that cisplatin-loaded OH-SWCNT nanocarrier complexes could target gastric CSCs and also could provide a potential strategy for selectively targeting and efficiently eliminating gastric CSCs. This could be a promising approach to prevent gastric cancer recurrence and metastasis and also improve gastric cancer therapy.