Meetings are expected to occur as early as postgame Sunday -- San Francisco hosts the Seahawks at 4:25 p.m. ET -- and no later than Monday, to determine their ultimate fates, sources said. But both Kelly and Baalke are said to know that their time in San Francisco is coming to an end.
The 49ers declined any comment.
Kelly has three years remaining on his contract; the Eagles also still will owe him a small portion, as well. Baalke, meanwhile, has two years left on his deal, but both men have gotten signals this could be the end.
It shapes up as another dramatic shakeup for the 49ers in which CEO Jed York and Executive Vice President Paraag Marathe will lead the search for replacements.
Kelly just finished his first season in San Francisco, which went 2-13 and finished last in the NFC West.
The Niners will become the first team since 1976-77 to fire coaches in back-to- back years after they had just one season at the helm. Coincidentally, the Niners were the last franchise to do it, firing Monte Clark and Ken Meyer after a single season on the job.
The Niners hired Kelly in January 2016 after firing Jim Tomsula, whom they hired in 2015 to replace Jim Harbaugh.
In nearly three full seasons with the Eagles, Kelly won 26 games and was only the second coach in Niners history to come aboard with previous NFL head-coaching experience.
None of that mattered much as Kelly's Niners flopped in 2016, dropping to the bottom of the league in a number of major categories and setting a franchise record with 13 consecutive losses.
Despite all of the struggles on the field, Kelly said as recently as this week that he was pleased with the group he had for his first year with the team.
"I look at, it's what you get to work with and I'm actually grateful for this group of guys we get to work with because of their attitudes and how they've approached it every single day," Kelly said.
"So, challenging is if maybe guys don't buy in or guys are doing things that are detrimental to the team and that hasn't happened here at all. This has been a great group to work with."
Information from ESPN's Nick Wagoner was used in this report.