Objective To assess the combined effect of consanguineous and child marriages (CCM) on children health, which has not previously been explored, either globally or locally. Methods We analyzed secondary data from a series of cross-sectional, nationally representative Pakistan Demographic and Health Surveys 1990–91, 2006–07, and 2012–13. A total of 5406 mothers with 10,164 children were included in the analysis. Child health was assessed by variables such as history of diarrhea, acute respiratory infection (ARI), ARI with fever, Under-5 child mortality (U5CM) and small-size birth (SSB). Associations among variables were assessed by calculating unadjusted Odd Ratios (OR) and adjusted OR (AOR). Results A majority (n = 6,247, 61%) of the births were to mothers having CCM as compare to non-CCM (3917, 39%). There was a significant association between CCM and U5CM during 1990–91 (AOR 1.24, 95% CI 1.03–1.49) and 2006–07 (AOR 1.25, 95% CI 1.05–1.51), and infant mortality in 1990–91 (AOR 1.39, 95% CI 1.05–1.85) and 2006–07 (AOR 1.61, 95% CI 1.17–2.21). A significant association was also found between CCM and SSB infants in the period 2006–07 (AOR 1.19, 95% CI 1.01–1.42) and 2012–13 (AOR 1.22, 95% CI 1.02–1.46). We noted no effect of CCM on diarrhea, ARI, and ARI with fever. Conclusion CCM increases the likelihood of U5CM, infant mortality and SSB infants. Further quantitative and qualitative research should be conducted to assess the effects of environmental, congenital and genetic factors on the health of children born to mothers in CCM.