Background In Tanzania Measles and Rubella (MR) vaccination coverage of 90% in 90% of the regions was achieved in 2018. However, there are councils lagging in MR1 coverage, 38 (19%) councils out of 195 had <90% coverage by the end of 2019 while MR2 coverage is struggling with 99 (51%) of councils having a coverage of <90% at the end of 2019. Kilimanjaro region is among the regions with some councils having MR coverage of <80%. There is a need for information on why a significant proportion of eligible children are not receiving the second dose of MR vaccine. Objective To determine prevalence and factors associated with incompletion of MR vaccination among children aged 18-59 months in two districts of Kilimanjaro region. Methodology This study was a cross-sectional study conducted in Moshi urban and rural councils, two out of the seven councils in Kilimanjaro region. The study population was children aged 18-59 months whose parents/ caregivers have been the residents of the respective districts for at least 3 past years. Interviews using questionnaires were used for data collection. Data was entered and analyzed using SPSS version 20. Results A total of 415 children aged 18-59 months were enrolled. The proportion of children with incomplete MR2 vaccination was 14.2%. Only 33% of the 415 caregivers knew MR vaccine is given at 9 and 18 months and 24% reported unavailability of vaccine at their scheduled visit. Children from Moshi rural council (AOR=2.53, 95% CI =1.36-4.73) had higher odds of MR incompletion. Lower odds of MR vaccine incompletion were among caregivers who were aware on the time for MR vaccination; 9 and 18 months (AOR=0.27, 95% CI=0.10-0.73), caregivers who had knowledge that MR vaccine protects measles, and those who had health promotion talk on the vaccination day. Conclusion Nearly one in ten (14.2%) children do not complete the recommended two doses of MR vaccines. Strategies to improve awareness and knowledge on timing, frequency and advantage of MR and other vaccines is needed among parents/ caregivers in this setting. Further, improvement in ordering and supply of vaccines at health facilities needs to be improved.