Lynch was predicted to be selected in the first round of the 2016 NFL Draft by draft analysts and in mock drafts prior to the draft. He was rated the third best quarterback in the 2016 draft by NFLDraftScout.com.
The Denver Broncos selected Lynch in the first round (26th overall) of the 2016 NFL Draft in a pick acquired from the Seattle Seahawks for their first and third round pick. He was the third of 15 quarterbacks taken, behind Jared Goff and Carson Wentz, the #1 and #2 overall picks. On June 9, 2016, the Broncos signed Lynch to a four-year, $9,476,296 contract with a $5,091,852 signing bonus.
On October 2, 2016, Lynch played in his first NFL regular-season game against the Tampa Bay Buccaneers, replacing the injured Trevor Siemian. He finished with 170 passing yards on 14 of 24 attempts and threw his first career touchdown pass to wide receiver Emmanuel Sanders in a 27–7 road win at Raymond James Stadium. In Week 5, Lynch started his first NFL game, completing 23 of 35 passes for 223 yards, one touchdown, and one interception in the 23–16 loss to the Atlanta Falcons. He was sacked six times, a record for a Broncos rookie. In Week 13, Lynch again replaced the injured Siemian against the Jacksonville Jaguars, posting 12 completions on 24 passing attempts for 104 yards in a 20–10 win. Overall, he finished his rookie season with 497 passing yards, two passing touchdowns, and one interception.