Background: Zika virus (ZIKV) infection has affected significantly Latin America in 2015–2017. However, most studies have been reported from Brazil and Colombia, but few of them in Central America. For these reasons we analyzed the incidence, incidence rates and evolution of cases of Honduras during 2016–2017. Methods: Using epidemiological weeks (EW) surveillance data on the ZIKV epidemics in Honduras, we estimated incidence rates (cases/100,000 population), and developed maps at national, departments and municipal levels. Results: From January 1, 2016 to December 31, 2017, a total of 32,607 cases of Zika were reported (98.5% in 2016 for an incidence rate of 36.85 cases/100,000 pop; 1% confirmed by RT-PCR). The highest peak was reached on the EW 6°, 2016 (2,559 cases; 29.34 cases/100,000 pop). The department with the highest number of cases and incidence rate was Cortés (13,128 cases, 791.08 cases/100,000 pop in 2016). Discussion: Pattern and evolution of Zika in Honduras has been like those that occurred for chikungunya in 2015, that we analyzed and previously reported, affecting predominantly the central and capital area of the country, reaching also high incidences there >750 cases/100,000 pop. Studies using geographical information systems, to map its epidemiology, as well on the clinical aspects linked to, are necessary in this country, as well for the assessment of risk for travelers who visit specific areas in a destination country.