Borja first ran for President of Ecuador in 1978, coming in fourth place.

He again ran for president in 1984, receiving the most votes in the first round, 36%, but he was defeated in the runoff.

He focused on Ecuador's economic problems during his presidency, and he increased collaboration with other countries in the Americas.

He spent time with U.S. President George H. W. Bush on 22 and 23 July 1990, even playing tennis with him.

It is claimed that he is a direct descendant of Pope Alexander VI through his son Giovanni Borgia, 2nd Duke of Gandia.