Later King George of Poděbrady of Bohemia appointed him to Lord Chamberlain of the District Court at Brno and in 1473 by the Anti-King Matthias Corvinus made him one of the four governors of Moravia.

Jan II is first mentioned in a document of 1427, when he and his father sold a piece of land to the abbess of the monastery Doubravník, which had been founded by Štěpán of Medlov, a predecessor of the Pernštejn family.

Prior to 1434, Jan II acquired the lien of Mitrov from Hynek Hlaváč, which he kept at least until 1448, as in that year an entry was made in Landtafel.

Jan opposed this; he and Hynce Ptáček of Pirkstein supported the candidacy of Casimir IV Jagiellon, the almost eleven-year-old son of King Władysław III of Poland.

In 1446, King George of Poděbrady made these liens into hereditary possessions of the Pernštejn family.

He made claims on lands in Tišnov which had belonged to the Porta coeli Convent before it was destroyed during the Hussite Wars.

King George of Poděbrady appointed Jan II in 1460 to Lord Chamberlain of the District Court at Brno.

A bible manuscript from the year 1471 in the National Library in Prague is richly decorated with illuminations and contains the coat of arms of Jan II of Pernštejn, suggesting that it was commissioned by him.