Multimammate mice (Mastomys natalensis) are a key rodent pest species to cereal crop production in Sub-Saharan Africa. This study aimed at generating information on the population fluctuation and breeding patterns of M. natalensis in a maize dominated agro-ecosystem in the Mayuge district, Eastern Uganda. The area is characterised by a bimodal rainfall pattern with rains in the periods March to May and August to November. A Capture–Mark–Recapture study was established in cultivated and fallow field habitats with, in each habitat, two plots of 60 m by 60 m with 49 evenly spaced trapping points. Trapping was conducted monthly for three consecutive nights, and the study extended from January 2016 to June 2018. A Generalised Linear Mixed Model analysis showed significantly higher population density estimates (β = 0.69, p < 0.0001) in fallow land compared to cultivated fields, and also significantly higher density estimates(β = 0.75, p = 0.006) in the first wet season and lowest in the first dry season. The percentage breeding females differed significantly across months (χ² = 27.05, df = 11, p = 0.003) and seasons (χ² = 17.64, p = 0.0003). Breeding females occurred throughout all the months of trapping, but with significantly higher percentages in the months of March to July (i.e. first wet season extending to second dry season) and generally lowest in the first dry months (i.e. January and February in 2017, and February 2018). The results of this study have important consequences for the timing of control efforts, and recommends that control should be initiated during the dry seasons prior to wet seasons to counteract potential damaging population build up in later wet seasons when crop planting is expected.