On June 23, 2016, Onuaku was selected by the Houston Rockets with the 37th overall pick in the 2016 NBA draft and later joined them for the 2016 NBA Summer League. On July 20, 2016, he signed with the Rockets. He made his NBA debut on December 26, 2016, coming on in the fourth quarter and recording six points and three rebounds in a 131–115 win over the Phoenix Suns. He hit a pair of free throws in the game with his underhanded free-throw action. During his rookie season, Onuaku had multiple assignments with the Rio Grande Valley Vipers, the Rockets' D-League affiliate. On May 1, 2017, he was suspended two games without pay for pushing a game official. The incident occurred during an altercation in the final seconds of the Vipers' 122–96 loss to Raptors 905 in Game 3 of the 2017 NBA D-League Finals on April 27.