Boxing star attacked corruption in government and singled out president Rodrigo Duterterelations with China in particular.
He was nominated by his political allies during the national assembly of the faction he leads within the ruling PDP-Laban party.
It comes days after a rival faction named Mr Duterte’s longtime aide Senator Christopher “Bing” Go as their presidential candidate.
The faction also appointed Mr Duterte as vice president, which critics have called a cynical attempt for Mr Duterte to retain power.
Mr. Go declined the nomination, and the divide between the factions that supported Mr. Pacquiao and Mr. Duterte deepened.
“I am a fighter, and I will always be a fighter in and out of the ring,” Mr. Pacquiao, 42, said during a speech broadcast live at the assembly.
“I accept your nomination as a candidate for President of the Republic of the Philippines. “
His faction has not expressed support for Mr Duterte’s candidacy for vice-presidency.
The country’s constitution prohibits the current president from running for a second six-year term.
Mr. Pacquiao is the only boxer to hold world titles in eight different divisions.
But despite his popularity, he lags behind in opinion polls which have always been dominated by Mr Duterte’s daughter, Sara Duterte-Carpio.
Mr. Pacquiao was elected leader of the PDP-Laban in July after challenging Mr. Duterte over his alliance with China and his track record in fighting corruption.
Mr Pacquiao was once a close ally of Mr Duterte, but said more than 10 billion pesos (£ 145,000) in pandemic aid to poor families remained untraceable.
He said it was only a discovery in his planned corruption investigation.
It comes as the Senate has opened an investigation into an alleged overpricing of medical supplies and equipment purchased by the government as part of its pandemic response program.
Mr. Duterte challenged Mr. Pacquiao to appoint corrupt officials, and Mr. Pacquiao responded by warning that the corrupt officials would go to jail.
He said, “Your time is up! ”