His parents were János Kovacsóczy, who fled from Slavonia due to the Ottoman invasion, and Erzsébet Török de Buda.
He married Kata Farkas de Harina first in 1581, three sons (including István) and two daughters were born.
He returned home in 1578 and was appointed Chancellor beside voivode Christopher Báthory, who took on state affairs on behalf of his brother.
In 1594, he strongly opposed the turn against the Ottomans and the alliance with the Habsburg Empire, along with Balthasar Báthory, cousin of prince Sigismund, and Sándor Kendi.
Farkas Kovacsóczy was strangled to death in the prison of Szamosújvár (today: Gherla, Romania) on 11 September 1594.