Globally, twice as many men as women are being diagnosed with tuberculosis (TB) annually. Little is known about gender differentials in TB in Africa. A retrospective cohort analysis of routine data was conducted on adult TB patients treated between 2011 and 2012 in two large healthcare facilities in Nigeria. Gender differences in their demographic characteristics and treatment outcomes were analysed accordingly. Of 1668 TB patients enrolled, the male:female ratio was 1·4:1. The mean ages of males and females were 40·2 ± 14·7 and 36·1 ± 14·6 years, respectively (t test 6·62, P < 0·001). Male gender was associated with a higher failure to smear convert after 2 months (21·8% vs. 17·5%, P = 0·06) and 5 months (4·3% vs. 1·5%, P = 0·02) of treatment for smear-positive TB patients. Moreover, men were more likely than women to fail treatment (2·2% vs. 0·7%, P = 0·01). No significant differences exist in the treatment success rates between women and men (78·2% vs. 74·5%, P = 0·08). Adjusted analyses showed significant association between being an urban male and a HIV-infected female with unsuccessful outcome adjusted by socio-demographic and clinical factors. We found that gender disparities exist in TB profile and treatment outcomes in Nigeria and gender-specific strategies are needed to optimize TB management.