On 23 June 2016, Siakam was selected by the Toronto Raptors with the 27th overall pick in the NBA draft, with the franchise signing him to a rookie scale contract on 9 July. On 2 October, he became the first rookie to start for the Raptors' season-opener since Jonas Valančiūnas did so in 2012; rising to the occasion, he hauled in 9 rebounds and notched 4 points in 21 minutes as Toronto beat the Detroit Pistons, 109–91. It marked not only his NBA debut, but the first NBA game that he had ever seen in person. On 3 December, Siakam scored a season-high 14 points, which came in a 128–84 victory over the Atlanta Hawks. On 1 January 2017, during a 123–114 win over the Los Angeles Lakers, he pulled down a season-high 10 rebounds.