To explore gender differences in food insecurity (FI) and minimum dietary diversity (MDD) among adolescent girls and boys in a slum community in Karachi, we employed an explanatory sequential mixed methods study that included a survey of 391 girls and boys of 10–19 years of age and followed by semi-structured interviews of eight purposely selected food insecure adolescents. Survey data was analyzed by Cox proportional algorithm and adjusted prevalence ratios (APR) with 95% confidence intervals (CI) were estimated for associated factors of FI and thematic analysis was undertaken for qualitative work. Meta inferences for mixed methods study were drawn by joint display analysis of survey results juxtaposed to qualitative findings. Overall, FI among adolescents was prevalent (46.5%) which was not different between boys (52.7%) and girls (47.3%) (APR 0.8, (95% CI 0.6, 1.2); p-value-0.4). MDD (5/10 food groups consumed) was achieved by only 23.0% and it was also not different between boys (25.1%) and girls (20.9%) (p-value-0.3). The survey found no significant difference in FI and MDD between boys and girls however, qualitative findings provided insight into the cultural practices at mealtimes that prefer boys. Qualitative results contrasted the survey results and revealed the increased vulnerability of girls towards FI and low MDD compared to boys due to gender norms.