Summary Background In patients with chronic hepatitis B (CHB)‐related hepatocellular carcinoma (HCC), high viral load was associated with tumour recurrence and deaths. Aims To investigate the effect of nucleos(t)ide analogues (NA) on the clinical outcomes after different HCC treatments. Methods A territory‐wide cohort study was conducted using the database from Hospital Authority. We identified CHB patients with HCC by International Classification of Diseases, Ninth Revision, Clinical Modification (ICD‐9‐CM) diagnosis codes in 2000–2012. HCC treatments, NA use and laboratory parameters were retrieved. The primary endpoint was HCC recurrence and death. A 3‐month landmark analysis was used to evaluate the primary outcome in patients with or without NA treatment. Results A total of 2198 CHB patients (1230 NA‐untreated and 968 NA‐treated) with HCC, receiving at least one type of HCC treatment were included in the analysis. At a median follow‐up of 2.8 (IQR 1.4–4.9) years, tumour recurrence and death occurred in 451 (36.7%) and 578 (47.0%) untreated patients; and in 216 (22.3%) and 301 (31.1%) NA‐treated patients respectively. NA therapy reduced the risk of overall HCC recurrence adjusted sub‐hazard ratio (SHR) 0.63, 95% confidence interval (CI) 0.49–0.80; P < 0.001. The effect was most obvious in patients undergoing resection (SHR = 0.58, 95% CI = 0.37–0.91, P = 0.018). The possibility of NA therapy reducing the risk of death (HR = 0.82, 95% CI = 0.64–1.03, P = 0.092), is most obvious in resection subgroup (HR = 0.64, 95% CI = 0.41–0.99, P = 0.050) but insignificant in the other treatment groups. Conclusion Our findings show that nucleos(t)ide analogues treatment reduces the risk of HCC recurrence in patients with chronic hepatitis B treated by surgical resection.