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Background Worldwide, success rates for quitting smoking have been stagnant for decades despite advancement in pharmacotherapy. This study aims to test the effectiveness of a current smoking cessation treatment programme which implemented the modified UK Standard Treatment Plan based on the NHS Centre for Smoking Cessation and Training (NCSCT). Methods We conducted a double-arm, cluster-randomised controlled trial with 1-month, 3-months and 6-months follow-ups among newly registered smokers seeking quit smoking services from 19 public hospitals in Malaysia. Smokers were assigned to either NCSCT behaviour modification (treatment group; n = 330) or usual care (control group; n = 172). The intervention was administered by dedicated health staff trained in the NCSCT. Data was collected through self-administered questionnaires, with validation conducted using expired air carbon monoxide measurement. Intention-to-treat analysis was adopted, with smokers who did not return for follow-ups considered smoking. Multiple logistic regression was conducted using a backward elimination model to assess the repeated measures treatment effect of quitting for each point of follow-up. Results No significant difference was discernible between the intervention and control group other than: first cigarette of the day (p=0.05), urge to smoke (p=0.020), method of quitting (p=0.018) and COppm level (p=0.0234) at baseline. Compared to the control group, individuals from the intervention group were more likely to quit successfully at 1-month, 3-months and 6-months follow-up (OR=1.698, OR=3.395, and OR=3.506 respectively). Older individuals were also more likely to abstain at 1-month, 3-months and 6-months follow-up (OR= 1.015, OR=1.022 and OR=1.032 respectively). Individuals who smoked at home were less likely to abstain at 1-month, 3-months and 6-months follow-up (OR= 0.637, OR=0.592 and OR=0.385 respectively). Conclusions The modified Standard Treatment Programme appears superior to routine care practice in maintaining follow up sessions among smokers due to its structured and organized sessions.