Castro, the country's first female president, took office last year after running on the promise of rolling back the country's restrictive reproductive policies.
Honduras, a heavily Catholic nation, banned the use and sale of the morning after pill in 2009, arguing the emergency contraception would cause abortions.
Castro, who signed the order on International Women's Day, tweeted that the morning after pill was "part of women's reproductive rights, and not abortive," citing the World Health Organization.
The year before Castro took office, Honduras' Congress passed a constitutional reform to protect anti-abortion laws, requiring a three-fourths vote to change them.
Between 50,000 to 80,000 clandestine abortions occur each year in the country, according to a 2019 estimate from local rights groups.