Background Despite presence of hyperendemic areas, the national immunisation schedule in Pakistan does not include a hepatitis B birth dose, placing newborns at an additional risk of acquiring hepatitis B. This study aimed to assess the impact of adding hepatitis B birth dose in existing national vaccination schedule. Methods An open label, randomised controlled non-inferiority trial enrolled 296 healthy near-term mothers to intervention and control groups. Newborns in the intervention group received a hepatitis B birth dose along with routine immunisation vaccines, while control group newborns received vaccinations under the national schedule. Seroprotection was measured and compared at birth and 8 weeks after administering the third dose of pentavalent vaccine. The risk ratio of seroprotection was computed and compared with the delta value set at 5%. Results The study found that 95.8% of infants in the intervention group achieved seroprotection, which was significantly higher than the control group’s 58.7%. The difference in risk ratio of seroprotection was 1.62 (CI95: 1.37–1.93), with the upper limit of the CI below the delta margin, confirming non-inferiority. The time interval between birth and the first hepatitis B immunisation shot was a predictor of seroprotection, with an odds ratio of 1.79 (CI95: 1.01–2.9). Conclusion Our study indicates that adding a hepatitis B birth dose to the immunisation schedule in Pakistan is non-inferior to the existing one. This can also contribute towards Pakistan’s achievement of the SDG target of reducing hepatitis B surface antigen seroprevalence in children under 5 years of age. Trial Registration Number NCT04870021