After the triumph of Alberto Fujimori in the general elections of 1990, Boloña was invited by Rodríguez-Pastor to a meeting in Miami with the president-elect and members of the economic team such as Adolfo Figueroa, Felipe Morris and Hernando de Soto.
Days later, Fujimori offered him the position of Minister of Economy and Finance, which he did not accept because part of the team in charge of the Central Reserve Bank would be appointed only by the president.
On 15 February 1991, Alberto Fujimori appointed him as Minister of Economy and Finance after the resignation of Juan Carlos Hurtado Miller.
As minister, he applied a series of liberal policies to overcome the crisis in the Peruvian economy such as the privatization wave, monetary, labor, trade and finance reforms.
He resigned from the ministry in January 1993, due to the delay in signing an agreement of intent between Peru and the International Monetary Fund.
His participation in politics has been discussed, especially because of his appearance in videos negotiating the possibility of carrying out a coup d'état supported by Vladimiro Montesinos, then head of the Peruvian intelligence services.