Broussonetia papyrifera has been identified as one of the top invasive species in some African tropical forests with potentially devastating impacts on the conservation and timber production potential of the forests. This study determined the effect of B. papyrifera on the regeneration of selected native timber species in Mabira Forest Reserve, Uganda. The abundance, basal area and population structure of the timber species were compared between areas invaded and uninvaded by B. papyrifera. Employing a complete randomized block design, a total of forty plots (30 x 30 m each), and equally distributed between invaded and uninvaded areas with similar habitat conditions were surveyed. Counts of seedlings were recorded and diameter of saplings and trees measured. Generalized linear models were used to analyze the abundance, tree basal area and size class distributions of the selected species. The study revealed that the effects of B. papyrifera invasion vary depending on the growth stage and species studied. Overall, B. papyrifera invasion significantly reduced tree abundance and basal area, and suppressed the regeneration of some but not all the selected species. Our results demonstrate that if the spread of B. papyrifera is not abated, it will lower the conservation and timber production potential of tropical forests. Therefore, we call for interventions to control the spread of B. papyrifera to the uninvaded parts of the forests and halt its multiplication in invaded areas so as to enhance the regeneration and growth of timber species.