[13] On July 6, 2012, Motiejūnas signed a four-year, rookie scale contract with the Houston Rockets[14] and joined them for the 2012 NBA Summer League.

[15] After the game, he quoted a famous Lithuanian idiom describing his debut: "Jeigu bijai vilko – neik į mišką" (English: If you're scared of wolves, don't go into the woods).

In August 2014, Motiejūnas came under fire for comments made about his Rocket teammates James Harden and Dwight Howard, describing their relationship as "Hi & bye.

[26] Then, even with Howard's return on December 13, Motiejūnas scored a then career-high 25 points on 11-of-19 shooting to help the Rockets defeat the Denver Nuggets, 108–96.

[29] However, the injury later ruled him out for the rest of the season[30] and put his chances of playing for the Lithuanian national team in doubt.

[31] In his third NBA season, Motiejūnas led the league in post-up field goal percentage (53.4%), with his biggest competitor being fellow Lithuanian Jonas Valančiūnas of the Toronto Raptors (51.3%).

[33] On December 1, 2015, Motiejūnas was cleared to return to practice, having been out since March 2015 after requiring surgery to repair a herniated disk in his back.

[34] Four days later, he returned to the Rockets' line-up and made his season debut, earning a standing ovation when he entered the game for the first time during the first quarter of the team's 120–113 win over the Sacramento Kings.

In the first round of the playoffs, the Rockets faced the first-seeded Golden State Warriors, and in a Game 3 win on April 21, Motiejūnas recorded 14 points and 13 rebounds for his first career double-double in the postseason.

[45] A day after the Rockets matched his four-year offer sheet to retain him, Motiejūnas did not show up for his scheduled physical exam with the team.

[51] He made his debut for the Pelicans four days later, recording 11 points and five rebounds in 20 minutes off the bench in a 117–108 loss to the Boston Celtics.

He initially appeared in 21 consecutive games after signing with New Orleans, but from February 25 through April 4, he logged 11 DNPs out of a 20-game span.

[53] On August 9, 2017, Motiejūnas signed a one-year, $2.2 million contract with the Shandong Golden Stars of the Chinese Basketball Association.

[55] On February 1, 2018, Motiejūnas recorded a triple double leading his team to an important 127–103 victory versus the Jiangsu Dragons by scoring 29 points, grabbing 15 rebounds and dishing out 10 assists.

[56] On March 13, 2018, Motiejūnas began the 2018 CBA Playoffs with 24 points, 7 rebounds and a victory versus the Jiangsu Dragons 104–100.

His team tied the series 2–2 after Motiejūnas solid contribution of 35 points (a career-high in China) and 14 rebounds versus his direct opponent Ioannis Bourousis.

[59] Despite his yet another astonishing performance of 31 points, 13 rebounds, 2 blocks and one assist, his team was eliminated in the series 3–4 after losing a decisive game 95–105.

[62] On March 3, 2019, Motiejūnas scored a career high 43 points, grabbed 17 rebounds, dished out 6 assists and led his team to a 122–83 victory.

Motiejūnas led Lithuania's junior national team to the silver medal at the 2008 FIBA Europe Under-18 Championship.

[76] In June 2015, Motiejūnas ruled himself out of the 2015 FIBA EuroBasket to continue recovering from a back injury he sustained while playing for the Houston Rockets.