Fertility among rural women in Uganda continues to decline. Studies on fertility in Uganda have focused on the overall fertility in the country. In this study, we focus on determinants of change in fertility among rural women in Uganda using a multivariate Poisson decomposition technique to quantify the contribution of changes in the socioeconomic and demographic composition of women which we also refer to as the characteristic effects and changes in their fertility behavior (the coefficients’ effects or risk of childbearing) to the overall reduction in fertility among women in rural areas during the 2006–2016 period. The “characteristics effects” are used to mean the effect of changing composition of women by the socioeconomic and demographic characteristics between 2006 and 2016. On the other hand, fertility behavior also presented as coefficients’ effects mean changes in the risk or likelihood of giving birth to children by the rural women between the two survey years. Our findings indicate that the mean number of children ever born (MCEB) reduced from 4.5 to 3.9 in 2006 and this reduction was associated with both the changes in composition of women and fertility behavior. The composition of women contributed to 42% while the fertility behavior contributed to 58% of the observed reduction. The education level attained and the age at first sex showed significant contributions on both components of the decomposition. The observed decline in fertility is largely associated with the variation in the risk of childbearing among the rural women. The variation in the risk of childbearing by education and age at first sex of the rural women showed to be the biggest contribution to the observed change in fertility. Continued improvements in access, attendance, and completion of secondary schools by women in rural areas will be the key drivers to Uganda’s overall transition to low fertility. Furthermore, with improved access to mass media in the rural areas, there can be changes in attitudes and large family size preferences which can create a conducive environment for the utilization of family planning services in the rural communities. Efforts should therefore focus on applying appropriate methods to deliver packaged family planning messages to these communities.