This study investigated factors affecting women’s participation in primary school headship position. The study’s sample comprised nine female and nine male head teachers, 35 female and 33 male teachers, 48 (24 female and 24 male) Standard 8 pupils from 18 primary schools in Lilongwe District, and six key informants. The head teachers and key informants were purposively selected while the teachers and pupils were randomly sampled. A questionnaire for head teachers and teachers, a focus group discussion guide for pupils, and an interview guide for key informants were the main data collection tools used. The qualitative and quantitative data collected were analysed manually and by using SPSS, respectively. The study established that, although they aspire for headship position and even where they outnumber male teachers as is the case in Lilongwe District, females are under represented in that position. The results show that socialisation and the devaluation of women’s work are the major explanatory factors from which stem other factors such as communities’ negative attitude towards female teachers; delayed promotion of female teachers; and assignment of female teachers to junior classes. Female head teachers face several challenges including insubordination from fellow teachers and working in hostile communities that expect them to behave like men. The study concludes that if women’s participation in headship position is to improve, it is necessary that the challenges facing female teachers be addressed. This should be through implementing existing policies and taking affirmative action aimed at improving the status of women in general and female teachers in particular.