Measles cases reported in Somaliland was 1,717 in 2012, of which 1,200 (69.8%) were from Burao district. With children population of 60,000, about 42,000 children in Burao district were not immunized for measles. While the facts of low measles immunization coverage were undisputable, the challenges facing measles immunization in Burao district remained largely un-documented. This study determined the challenges facing measles immunization coverage for 9 - 59 months old children in Burao district, Somaliland. Guided by the Herd Immunity Theory, and based on a cross-sectional survey of a two-stage cluster sample of 383 parents/caregivers, data was collected using questionnaire and interview method in April 2015. The study found that that immunization of 9 - 59 months old children in Burao district did not depend on access factors (χ2 [8, N = 383] = 3.072, p = .881). But it was significantly dependent on awareness factors (χ2 [8, N = 383] = 215.990, p = .023, C = .600); and on conception of immunization (χ2 [8, N = 383] = 145.634, p = .018, C = .524). The study concluded that awareness is the major challenge facing immunization for 9 - 59 months old children in Burao district.