Pongračić started his football career as a product of Bayern Munich academy, before moving to FC Ingolstadt 04 in 2013 at the age of 16.

[3] On 29 August 2018, in a Champions League qualifying play-off return leg against Red Star Belgrade, with Salzburg 2–0 up on the night and seemingly comfortably headed towards Champions League qualification, Pongračić received a 63rd-minute yellow card for fouling Milan Pavkov by stomping on him.

"[10][11] On 21 February 2019, he provided Patson Daka with an assist for the second goal as Salzburg defeated Club Brugge 4–0 in Europa League round of 32.

[13] After the injury-stricken stint at Salzburg, Pongračić joined VfL Wolfsburg on 15 January 2020 on a four-and-a-half-year deal for a fee believed to be €10 million.

[14][15] On 8 February, in his second appearance for the club, he was sent off after elbowing Alfredo Morales, as Wolfsburg drew 1–1 with Fortuna Düsseldorf.

[18] After he missed the beginning of the new season due to mononucleosis, Pongračić returned to the team on 8 November as an injury time substitute for Xaver Schlager in the 2–1 victory over 1899 Hoffenheim.

[28] He received his first call-up for the senior team on 17 August 2020 for September Nations League fixtures against Portugal and France.

His parents Stribor and Anđelka fled from Slavonski Brod, Croatia to Germany during the Croatian War of Independence.

[28][39] Pongračić named Kalidou Koulibaly and Virgil van Dijk his football idols.