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Lee did not receive a restricted free agent tender from the 49ers after the 2019 season, and he became a free agent on March 18, 2020.

On April 1, 2020, Lee signed with the Detroit Lions.

Lee announced his decision Friday afternoon via Twitter.“After talking with my family and going through the tough times we have experienced this opportunity is something I can’t pass up,” Lee wrote. “At this time I will forgo my senior season and enter the upcoming 2017 NFL draft. I am looking forward to this opportunity and appreciate everyone’s support going forward.”

On August 31, 2019, Lee was waived by the 49ers and was signed to the practice squad the next day. He was promoted to the active roster on November 5. Lee reached Super Bowl LIV with the 49ers, but lost 31-20 to the Kansas City Chiefs.

Lee was drafted by the Minnesota Vikings in the seventh round, 232nd overall, in the 2017 NFL Draft. "I'm just proud to be a Viking," Lee said after his selection. "That was one of my favorite teams and one of my top priorities, too, because they showed so much love and also because there's Kansas State alums." He was waived on September 2, 2017, and was signed to the practice squad the next day.

On September 13, 2017, Lee was signed by the San Francisco 49ers off the Vikings' practice squad.

Lee started all 13 games as a sophomore in 2015, leading the team with 80 tackles en route to second-team All-Big 12 honors from the league’s coaches, becoming Kansas State's first underclassman linebacker to earn either first or second-team All-Big 12 honors since College Football Hall of Famer Mark Simoneau back in 1998. He was also the first Wildcat underclassman to lead the team in tackles since 2008. He finished second on the team with 7.5 tackles for loss and third with 5.0 sacks, and recorded three interceptions, the most by a linebacker since 2002. Two of his picks came against TCU on in week 5, and were the most in a game by a Wildcat linebacker since 2002. In the game against Louisiana Tech, he set career highs in tackles with 12, tackles for loss with 3.0 and sacks with a pair. He also reached double digits in tackles against Texas Tech with 11 (including a 14-yard sack). Lee also earned second-team Academic All-Big 12 honors.

As a freshman in 2014, Lee played in all 13 games and totaled 19 tackles, including 4.5 sacks, a forced fumble and a pass breakup. His 4.5 sacks were the most sacks by a true freshman in school history and the second-most among all freshmen (true and redshirt), and also the most among all true freshmen in the Big 12 in 2014. He started the season off with two sacks against Stephen F. Austin, becoming the first true freshman under head coach Bill Snyder to record two sacks in a game. Against UTEP in week 4, he registered a season-high four tackles. He recorded sacks against Texas and Kansas, and a half sack at Iowa State.

Lee was regarded as a three-star recruit by Rivals.com and was rated the 39th-best outside linebacker nationally by Scout.com and 41st by Rivals. Lee committed to Kansas State on March 26, 2013. He also had scholarship offers from Iowa and Nebraska, among others.

Lee attended Blue Springs High School, where he played football under head coach Kelly Donohoe. He was a teammate of current Kansas State running back Dalvin Warmack. During his high school career, Lee was a two-time Kansas City Star All-Metro honoree and was a two-time recipient of the Buck Buchanan Memorial Award, given to the best lineman or linebacker in the top two high school classes in Kansas or Missouri high school football in the Kansas City area, being only the second two-time winner of the award. Lee was named to the MaxPreps Junior All-American team as a junior in 2012 after collecting 71 tackles, 33.5 tackles for loss and 18.5 sacks. He was also a first-team All-State honoree by both the coaches and media. As a senior in 2013, Lee recorded 85 tackles, including 36 for loss and 12 sacks. He was selected as the Missouri Football Coaches' Association (MFCA) Class 6 Defensive Player of the Year, while he was a unanimous pick for the MFCA All-State squad. He was also named first-team All-State by the Missouri media and was selected to the USA Today All-USA Missouri Team. Lee also participated in basketball, earning all-conference and all-district honors, and track and field at Blue Springs.

Lee made the transition from defensive end in high school to outside linebacker at Kansas State. A three-year letter winner, Lee became the first Wildcat linebacker to earn consecutive All-Big 12 honors since Arthur Brown in 2011 and 2012. Lee finished his collegiate career with 209 total tackles (153 solo), 18.5 tackles for loss, 11 sacks, 5 forced fumbles and five interceptions (the most by a Wildcat linebacker under head coach Bill Snyder). He is also tied for fourth in Kansas State bowl history with 20 career tackles. During his time at Kansas State, the Wildcats had a 24–15 record and three bowl berths prior to declaring to the NFL Draft after his junior year.

Elijah James Lee (born February 8, 1996) is an American football linebacker for the Detroit Lions of the National Football League (NFL). He played college football at Kansas State, and was drafted by the Minnesota Vikings in the seventh round in the 2017 NFL Draft.