He was born as the second child to a lower noble family in Orava (region). He studied at a grammar school (gymnasium) in Ružomberok (Rózsahegy) 1774-78, and later in Trnava (Nagyszombat) and Vienna, and graduated in theology at the general seminary in Pressburg (present-day Bratislava) in 1787. In the very same year, he codified the first Slovak language standard, which he based on western Slovak dialects spoken around Trnava, with some elements from the central dialects. The language, called bernolákovčina, wasn't accepted as a national standard language, although it was a milestone on the way to the formation of the modern Slovak nation. From 1787 to 1791, he was a curate in Čeklís (Cseklész, present-day Bernolákovo), from 1791 to 1797 a secretary in the archbishopric vicar's office in Trnava, and from 1797 until his death in 1813, a priest in Nové Zámky).
His language was the basis for the activities of the Slovenské učené tovarišstvo (Slovak Educated Brotherhood), established in 1787 in Trnava, and also for the movement of Bernolák's followers, which lasted three generations. Exhaustive literary and priestly work, concern about his close family and other circumstances undermined his health to such an extent that he died unexpectedly of a heart attack on January 15, 1813.
