This study examined maternal mental health in mothers of children with neurodevelopmental and genetic disorders in Pakistan; maternal education and affiliate stigma were also tested. It was hypothesised that mothers of children with neurodevelopmental and genetic disorders would experience high levels of depression, anxiety and affiliate stigma, and that these variables would be mediated by the level of maternal education. Seventy-five mothers of children with neurodevelopmental and genetic disorders were recruited from “Special Needs” schools in Lahore and Islamabad. The results showed that the majority of mothers were clinically depressed and a large majority of mothers were clinically anxious. The distribution of mothers with clinical anxiety was significantly different among mothers with different levels of education (p < 0.05). Furthermore, mothers with higher levels of education had less affiliate stigma. This result suggests that maternal education may be a protective factor of mental health in mothers of children with neurodevelopmental and genetic disorders. Limitations, implications and future research are discussed.