Affiliated to the populist Justicialist Party, the new administration of Carlos Menem appointed him Director of National Budget Policy for Provincial Spending.

Remaining in the post during the difficult transition of numerous important federal programs to provincial budgets, Fernández was appointed Undersecretary of Budgetary Policy for the Province of Buenos Aires, Argentina's largest, in 1997 by Governor Eduardo Duhalde.

Tapped as Economy Minister of the Province of Buenos Aires by Governor Felipe Solá in March 2007, he was returned to the President's office as Budget Director on Cristina Kirchner's inauguration in December of that year.

Following the 2008 Argentine government conflict with the agricultural sector, touched off by a proposed increase in export taxes, the economist's non-confrontational style helped lead to his 25 April replacement of the less conciliatory Martín Lousteau as Minister of the Economy.

[2][3] The ruling Front for Victory's defeat in the 28 June 2009, mid-term elections led to a cabinet reshuffle, and Fernández tendered his resignation to the President, effective July 7.