Discrimination and limited access to healthcare services in remote areas can affect vaccination coverage. Therefore, this study aimed to estimate vaccination coverage for children living in quilombola communities and rural settlements in the central region of Brazil during their first year of life and to analyze the factors associated with incomplete vaccination. An analytical cross-sectional study was conducted on children born between 2015 and 2017. The percentage of children who received all vaccines recommended by the National Immunization Program in Brazil by 11 months and 29 days was used to calculate immunization coverage. Children who received the following vaccines were considered as having a complete basic vaccination schedule: one dose of BCG; three doses of Hepatitis B, of Diphtheria-Tetanus-Pertussis (DPT), of type b (Hib), and of Poliovirus (Polio); two doses of Rotavirus, of 10-valent pneumococcal (PCV10), and of Serogroup C meningococcal conjugate (MenC); and one dose of Yellow Fever (YF). Measles-mumps-rubella (MMR) and other doses recommended at or after 12 months were not included. Consolidated logistic regression was used to identify factors associated with incomplete vaccination coverage. Overall vaccination coverage was 52.8% (95% CI: 45.5-59.9%) and ranged from 70.4% for the Yellow Fever vaccine to 78.3% for the Rotavirus vaccine, with no significant differences between the quilombola and settler groups. Notably, the likelihood of incomplete general vaccination coverage was higher among children who did not receive a visit from a healthcare professional. Urgent strategies are required to achieve and ensure health equity for this unique and traditionally distinct group with low vaccination coverage.