49ers’ McCaffrey signs two-year extension; Aiyuk absent at mandatory minicamp

SANTA CLARA — Christian McCaffrey and the 49ers agreed Tuesday to a two-year contract extension worth $19 million each season.

The deal, which will keep McCaffrey with the team through the 2027 season and keep him the NFL’s highest-paid running back, was first reported by ESPN’s Adam Schefter.

Meanwhile, the plot thickens regarding wide receiver Brandon Aiyuk, who along with tackle Trent Williams were the only absences Tuesday at the 49ers’ mandatory minicamp according to coach Kyle Shanahan. Aiyuk, in contrast to players with contract issues in previous years such as Fred Warner, George Kittle and Nick Bosa, determined his best course of action was not to attend.

Williams, Shanahan said, was expected Wednesday and was attending his daughter’s graduation while Aiyuk’s absence was related to “contract stuff.” In theory, the 49ers could fine Aiyuk slightly more than $100,000 as punishment for missing the mandatory camp although they’re not obligated to do so.

Although the session is termed “mandatory,” Shanahan downplayed the significance of Aiyuk’s absence.

“To me, it doesn’t change at all,” Shanahan said after Tuesday’s practice. “You can find out when guys are in those situations whether they come or not. Some guys come because they want to avoid a fine and some don’t. Regardless it doesn’t change anything. We know what the process is. We know what the business part is.”

When Bosa missed training camp a year ago while negotiating a contract, he was not fined.

McCaffrey’s status has been a mystery in that he missed all the voluntary sessions leading up to the mandatory camp. A year ago, McCaffrey was a pace- and tone-setter in voluntary workouts for the 49ers as they worked through quarterback Brock Purdy’s return from elbow surgery.

“Business is business. It’s part of this game,” McCaffrey said. “Both sides were mutually very respectful the whole time. Just proud and happy that we got something done.”

McCaffrey, 27, was scheduled to make $11.8 million in salary with a cap number of over $16 million on a deal negotiated in 2020 with the Carolina Panthers before the 49ers acquired him in October 2022. As the NFL’s Offensive Player of the Year last season, McCaffrey led the league with 1,459 yards rushing to go along with 564 receiving yards and 21 total touchdowns.

“He’s the same guy every day he walks into the building, the same guy on and off the field and we hope to have him here for a long time,” Shanahan said.

McCaffrey did not practice but joined teammates on the field late during the practice session. Shanahan said he doesn’t expect McCaffrey to practice Wednesday, either.

“There’s no substitute to being out on the field with the guys to practice football, but you do the most with what you have,” McCaffrey said.

It was important for McCaffrey to receive more money not only because of his performance but also because the running back position is generally near the bottom of the NFL salary structure because of attrition and the demands of the position.

“Running back has been undervalued for some time now and I think this is a step in the right direction,” McCaffrey said.

Aiyuk, 26, is scheduled to play under the fifth-year option of just over $14 million. Bosa was under a fifth-year option a year ago and reported to the mandatory minicamp although he didn’t participate. Bosa eventually landed a five-year, $170 million deal with $122.5 guaranteed that temporarily made him the NFL’s highest-paid non-quarterback at an average per year of $34 million.

That figure was surpassed Monday when Minnesota wide receiver Justin Jefferson received a four-year, $140 million extension ($35 million average) and it just happens to be at Aiyuk’s position.

There has been a glut of big-money contracts signed by wide receivers, including Detroit’s Amon-Ra St. Brown, Philadelphia’s A.J. Brown and DeVonta Smith, that range between $25 million and $30 million in average salary.

Aiyuk has steadily increased his production and last season caught 75 passes for 1,342 yards and seven touchdowns. Deebo Samuel, who had a contentious negotiation two years ago before agreeing to a three-year extension worth $23.8 million per season, said he’s been giving advice to Aiyuk.

“I know this is a stressful time. He’s done a tremendous job throughout his career here and when it comes to things like this it gets tough,” Samuel said. “Some things you kind of take personal and overall it’s stressful.”

Pearsall progress

First-round draft pick Ricky Pearsall practiced in a blue jersey “hands off” jersey. Shanahan explained it was a way to get his work in and to keep him healthy at the same after Pearsall was “sore” following last week’s OTA practices.

Pearsall seems to have developed an immediate connection with Purdy and is getting a lot of run with Aiyuk absent and Samuel taking limited reps.

“He’s got really good hands, we’re giving him a lot of reps, doing a lot of different routes, trying all the positions and we’ve been impressed with how he’s started off,” Shanahan said.

Thomas taking it in

Veteran tight end Logan Thomas will be a spectator this week after signing a free agent contract but will be looked upon to battle for a spot on the roster along with 2023 draft picks Cameron Latu and Brayden Willis, as well as Eric Saubert and Jake Tonges.

Logan caught 55 passes for 496 yards and four touchdowns for Washington. Neither Charlie Woerner nor Ross Dwelley is on the current roster after both signed this spring with the Atlanta Falcons.

“I just really wanted to up the competition with the group and bring a guy in with experience in the run and pass game,” Shanahan said. “We like our group and there’s some competition there. To be able to add a veteran like Logan and get him in here is something we’re pumped to pull off.”

Sitting it out

Players spotted rehabbing injuries included cornerback Charvarius Ward, Kittle, linebacker De’Vondre Campbell, rookie wide receiver Jacob Cowing, defensive tackle Jordan Elliott and Latu.

Shanahan conceded he was playing it safe given that he’d like as many players to go into their 40-day offseason as healthy as possible.

“You want all guys to work, but you can get hurt any time,” Shanahan said. “When guys haven’t been here through Phase 1, Phase 2, Phase 3, just to throw them out there, we’re not going to risk that. No matter what happens today or tomorrow, we’re going to get away and come back in 40 days.”