Scant evidence exists to identify the effects of the pandemic on migrant women and the unique barriers on employment they endure. We merge longitudinal data from mobile phone surveys with subnational data on COVID cases to examine whether women were left more immobile and vulnerable to health risks, relative to men, during the pandemic in Kenya and Nigeria. Each survey interviewed approximately 2000 men and women over three rounds (November 2020–January 2021, March–April 2021, November 2021–January 2022). Linear regression analysis reveals internal migrants are no more vulnerable to knowing someone in their network with COVID. Rather, rural migrant women in Kenya and Nigeria were less vulnerable to transmission through their network, perhaps related to the possible wealth accumulation from migration or acquired knowledge of averting health risks from previous destinations. Per capita exposure to COVID cases hinders the inter-regional migration of women in both countries. Exposure to an additional COVID case per 10,000 people resulted in a decline in women’s interregional migration by 6 and 2 percentage points in Kenya and Nigeria, respectively.