Abstract Background and Aim An accurate preoperative diagnosis as the basis for deciding the most appropriate surgical procedure is essential for patients with suspected gallbladder cancer (GBC). The aim of this study was to investigate the usefulness of cell‐free DNA (cfDNA) for the preoperative detection of ≥T2 invasion in patients with suspected GBC. Methods Twenty‐four patients who underwent resection for suspected GBC were enrolled. The concentration of cfDNA obtained from blood samples preoperatively was measured and evaluated in two distributions. The first peak (less than 200 base pairs) of cfDNA distribution was defined as the shorter fragment cfDNA, considered to originate mainly from apoptosis; and the second peak (200 base pairs or more) was defined as the longer fragment cfDNA, originating mainly from necrosis. Results Pathological analysis identified benign disease in 12 patients and GBC in 12 patients, of whom 6 patients had ≥pT2 GBC. Carcinoembryonic antigen (CEA) and carbohydrate antigen (CA)19‐9 were significantly higher in the ≥pT2 GBC group than in the benign/<pT2 groups (2.1 [0.7–11.0] vs 4.5 [1.7–13.0], P = 0.033 and 14.0 [<2.0–401] vs 37.0 [26.0–141.0], P = 0.007, respectively). When limited to patients in the GBC group (n = 12), only cfDNA of longer fragments was significantly lower in the ≥pT2 group than the <pT2 groups (2.98 [1.88–4.61] vs 1.98 [1.42–2.42], P = 0.026) but cfDNA of shorter fragments showed no significant difference between above both comparisons. Conclusion CfDNA might have potential use as a diagnostic factor for patients with suspected GBC.