On July 17, 2015, Marjanović signed a one-year, $1. 2 million contract with the San Antonio Spurs. He made his NBA debut on October 30, recording 6 points and 5 rebounds in the Spurs' 102–75 win over the Brooklyn Nets. On December 4, he was assigned to the Austin Spurs, San Antonio's D-League affiliate. He was recalled by San Antonio on December 6, and, the following day, scored 18 points on 8-of-10 shooting in a 119–68 win over the Philadelphia 76ers. On December 28, in a win over the Minnesota Timberwolves, Marjanović provided a spark off the bench with Tim Duncan out injured and LaMarcus Aldridge limited to six points. Marjanović scored 17 points on 7-of-7 shooting in just 14 minutes to help the Spurs defeat the Timberwolves 101–95 and extend their franchise-record home winning streak to 27 games (dating to 2014–15 season). Two days later, in a win over the Phoenix Suns, he became the first player in Spurs franchise history to record 12 rebounds in 15 minutes or less. On January 21, 2016, he recorded 17 points and a career-high 13 rebounds in a 117–89 win over the Phoenix Suns. On March 20, he was reassigned to the Austin Spurs, earning a recall two days later. On March 23, he scored a then career-high 19 points in a 112–88 win over the Miami Heat. On April 13, in the team's regular season finale, Marjanović recorded a career-high 22 points and 12 rebounds in a 96–91 win over the Dallas Mavericks.