Background: Children of Myanmar migrants in Thailand have lower immunization coverage compared to Thai counterparts, leaving them at risk of vaccine preventable diseases. Evidence remains limited regarding immunization among Myanmar children in Chiang Rai Province, an important migration corridor between Northern Thailand and Myanmar. Objective: this study aimed to estimate the immunization status and identify its associated factors among children of Myanmar migrants in Chiang Rai province, Northern Thailand. Methods: A cross-sectional study was conducted among Myanmar migrant caregivers and their children aged under 7 years, who are residing in Chiang Rai Province, using a validated questionnaire by face-to-face interview. Descriptive statistics was used to summarize participant characteristics, while chi-square tests and binary logistic regressions were used to identify associated factors with statistical significance set at α< 0.05. Results: Among 423 children, 91 children (21.5%) were found as having incomplete immunization and six factors were significantly associated with it, including lacking Thai birth registration (aOR = 9.52; 95% CI: 3.74–24.27), lacking child’s health insurance (aOR = 14.03; 95% CI: 6.45–30.54), history of return migration (aOR = 19.05; 95% CI: 8.48–44.13), negative peer practices (aOR = 8.09, 95% CI: 1.47–44.54), time barrier (aOR = 4.09, 95% CI: 1.20–13.94) and financial barrier (aOR = 7.07, 95% CI: 1.67–29.91). Conclusions: A moderate prevalence of incomplete immunization was strongly associated with factors across the levels of the modified socio-ecological model: intrapersonal, interpersonal, and institutional. Interventions addressing legal access, health insurance, community outreach, healthcare system responsiveness and cross-border continuity of care are recommended.