This study aims to examine differences in cognitive impairment and mobility disability between older men and women in Ouagadougou, Burkina Faso, and to assess the extent to which these differences could be attributable to gender inequalities in life course social and health conditions. Data were collected on 981 men and women aged 50 and older in a 2010 cross-sectional health survey conducted in the Ouagadougou Health and Demographic Surveillance System. Cognitive impairment was assessed using the Leganés cognitive test. Mobility disability was self-reported as having any difficulty walking 400 m without assistance. We used logistic regression to assess gender differences in cognitive impairment and mobility disability. Prevalence of cognitive impairment was 27.6% in women and 7.7% in men, and mobility disability was present in 51.7% of women and 26.5% of men. The women to men odds ratio (95% confidence interval) for cognitive impairment and mobility disability was 3.52 (1.98–6.28) and 3.79 (2.47–5.85), respectively, after adjusting for the observed life course social and health conditions. The female excess was only partially explained by gender inequalities in nutritional status, marital status and, to a lesser extent, education. Among men and women, age, childhood hunger, lack of education, absence of a partner and being underweight were independent risk factors for cognitive impairment, while age, childhood poor health, food insecurity and being overweight were risk factors for mobility disability. Enhancing nutritional status and education opportunities throughout life span could prevent cognitive impairment and mobility disability and partly reduce the female excess in these disabilities.