According to the French news agency AFP, Duterte submitted his candidacy at the Commission on Elections office, minutes before the deadline to join the race.
Duterte, who is constitutionally barred from seeking a second six-year term, was elected as President in a general election in 2016.
He previously said he would run for the country's second-highest office, before changing his mind and announcing plans last month to retire from politics.
He made a similar declaration in September 2015, saying he "will retire from public life for good", only to announce a presidential bid two months later.