In 2015, the Zika virus was introduced in Colombia. The emergence of this arbovirus is a public health challenge for the country, considering the association between the infection and congenital disorders such as microcephaly. Thus, we estimated the burden of disease due to microcephaly associated with Zika in Colombia and its administrative subdivisions for the period 2015-2016. We conducted an exploratory ecological study, using as unit of measurement disability-adjusted life years (DALYs). The cases of microcephaly were obtained from the Zika national and departmental databases built by the National Public Health Surveillance System (SIVIGILA). Deaths attributed to microcephaly were estimated from previous studies. Finally, we calculated mortality rates and incidences, then we performed a sensitivity analysis under three scenarios (conservative, medium, and extreme) to estimate the DALYs. In the 2015-2016 period, 10,609.4 DALYs were caused by microcephaly associated with Zika in Colombia. 71% of the total DALYs were years of life lost and 29% were years lived with disability. Five out of 32 departments (Meta, Córdoba, Tolima, Valle del Cauca, and Norte de Santander) contributed 71% of total DALYs. The burden of microcephaly associated with Zika outweighed the burden of other congenital anomalies such as neural tube defects and Down syndrome in children aged between 0 and 4 years in Colombia. Public health efforts must be made to prevent and monitor these cases.