Toward 2019, Uganda experienced an extensive outbreak of measles and rubella. The Uganda National Expanded Programme on Immunization implemented a mass measles-rubella vaccination campaign aimed at halting the ongoing transmission. This study determined the changes in the disease burden thereafter. We conducted a retrospective cross-sectional study on measles-rubella positivity and its associated factors in Uganda using 1697 case-based surveillance data for 2019 and 2020 stratified into two dispensations: prevaccination and postvaccination campaigns. Statistical tests employed in STATA 15 included chi-square, Fisher’s exact, and binomial tests. Measles positivity rates in the period before and after the mass immunization campaign were 41.88% (95% CI: 39.30–44.51) and 37.96% (95% CI: 32.81–43.40), respectively. For rubella, the positivity rate in the precampaign season was 21.73% (95% CI: 19.61–23.99) and in the postvaccination season was 6.65% (95% CI: 4.36–10.00). Binomial tests indicated that postcampaign positivity rates were significantly lower than the precampaign rate for measles (
p
=
0.003
) and rubella (
p
<
0.001
). Generally, age (χ2 = 58.94,
p
=
0.001
/χ2 = 51.91,
p
<
0.001
) and vaccination status (χ2 = 60.48,
p
=
0.001
/χ2 = 16.90,
p
=
0.001
) were associated with the measles positivity rate in both pre/postcampaign periods. Rubella positivity rate was associated with vaccination status (χ2 = 32.97,
p
<
0.001
/
p
=
0.001
) in both periods and age in the precampaign season (
p
<
0.001
). The measles-rubella mass campaign lessened rubella burden remarkably, but barely adequate change was observed in the extent of spread of measles. Children aged less than 9 months are at higher chances of testing positive amidst low vaccination levels among the eligible. The immunization programme must attain and maintain routine immunization coverage at 95% or more and roll out a second-dose measles-rubella vaccination to sustain the reduced disease burden.