Gissur was the son of Einar Sigvaldason on Hraun í Landbroti and of Gunnhildur Jónsdóttir. He was the nephew of Halldóra Sigvaldadóttir. He attended Skálholt's school where he was instructed by bishop Ögmundur Pálsson and went to study further at Hamburg, where he discovered Protestantism. He was made a priest shortly after he came back to Iceland, and Ögmundur chose him as his successor in 1539. The king ratified this decision the following year, yet he was not formally made into bishop until 1542, in Copenhagen.
On October 7, 1543, Gissur married Katrín Hannessdóttir, sister of Eggert Hannesson.