Woerner was drafted by the San Francisco 49ers in the sixth round with the 190th overall pick in the 2020 NFL draft.[7] The 49ers previously acquired this pick after trading wide receiver Marquise Goodwin to the Philadelphia Eagles.[8] Woerner was placed on the reserve/COVID-19 list by the 49ers on December 19, 2020,[9] and activated on December 29.[10] He finished his rookie season with 3 catches for 36 yards on 4 targets in 14 games and emerged as a skilled blocking tight end in both pass blocking and run blocking.
In the 2021 season, he played all 17 games and finished with 5 catches for 52 yards on 6 targets while in 2022 he played in all 17 games and did not record any catches. He continued to be a skilled blocker for the 49ers in those two seasons, with a 75.4 run blocking grade and a 74.3 pass blocking grade from Pro Football Focus in 2021.
In the 2023 season, Woerner recorded 3 catches for 32 yards on 3 targets and played in all 17 games. He also notably finished the season with the third highest PFF run-blocking grade among tight ends for the 2024 season with a grade of 76.8.
Atlanta Falcons
On March 13, 2024, Woerner signed a three-year deal with the Atlanta Falcons worth 12 million dollars.[11] He was signed following the Falcons' release of Jonnu Smith to be paired with returning tight end Kyle Pitts as the team's new tight end duo with Pitts being the team's main receiving tight end and Woerner being the team's main blocking tight end.