Background Understanding the incidence of laboratory-confirmed measles virus (MV) cases, related factors, and spatial inequalities in testing and surveillance is crucial to proving evidence-based decisions in measles prevention and control programs. In this analysis, our aim was to evaluate these factors in Eritrea.Methods Reviewed and analyzed a disease surveillance database from 2002 to 2020, used descriptive statistics and logistic regression, and calculated spatial variability and distribution of confirmed cases using ArcGIS Pro version 3.0.1 with a significance level of 5%.Results The median age (IQR) was 7 years (4–14 years) and the minimum-maximum age was 1 month – 97 years. In total, 9,111 suspected cases, 2,767 (1,431 (51.7%) females vs 1,336 (48.3%) males) were serologically tested. Among the 608 (21.9%) laboratory-confirmed cases, 534 (87.8%) were unvaccinated and 53 (9.92%) were < 1 year old. The crude incidence rate (CIR) for MV was 14/100,000 persons. The age-specific positivity rate per 100,000 suspected cases tested was 21.5 with individuals > 30 years presenting the highest rates, 69.9/100,000. The probability of test positivity was associated with an increasing age at the beginning of the rash (5–9 years: OR = 0.7, 95%CI: 0.5–0.9, p value = 0.02) (10–14 years: OR = 1.6, 95%CI: 1.1–2.2, p value = 0.005) (15–29 years: OR = 7, 95%CI: 5.3–9.2, p-value < 0.001) ( > = 30: OR = 16.7, 95%CI: 11.7–24, p-value < 0.001); Address (Anseba: OR = 2.3, 95%CI: 1.7–3.1, p-value < 0.001) (Debub: OR = 2.7, 95%CI: 1.9–3.9, p-value < 0.001) (Gash-Barka: OR = 15.4, 95%CI: 10.9–21.7, p-value < 0.001) (Northern Red Sea: OR = 11.8, 95%CI: 8.5–16.2, p-value < 0.001) (Southern Red Sea: OR = 14.4, 95% CI: 8.2–25.2, p-value < 0.001); Health facility (Health centre: OR = 2.5, 95%CI: 1.9–3.4, p-value < 0.001) (Hospital: OR = 6.8, 95%CI: 5.1–9.1, p-value < 0.001); Vaccination status (Unvaccinated: OR = 14.7, 95%CI: 11.4–19.1, p-value < 0.001); and year of onset of rash (2015: OR = 1.4, 95% CI: 1.1–1.7, p-value < 0.001). Interestingly, uptake of the measles vaccine (MCV) coverage was associated with a similar complement of factors.Conclusion The study concludes that efforts to eliminate measles in Eritrea are hindered by disparities in vaccine coverage and surveillance, and low vaccination rates in neighboring countries. The paper suggests that regional microplanning could be an effective strategy to improve surveillance and management in hard-to-reach regions.