A source also told Schefter that the Niners,who are looking for a new coach for the second straight year, will meet withCleveland Brownsoffensive coordinator John DeFilippo on Friday.
CSNBayArea.com earlier reported, citing sources,that Kelly and Lynn met with the 49ers on Thursday.
Kelly was fired by the Eagles on Dec. 29 with one game remaining in the season and the team sporting a 6-9 record. Kelly, who sources indicate would like to remain in the NFL, was 26-21 in three seasons with the Eagles.
Kelly's camp had reached out to the 49ers to express interest in the job, a league source told Schefter on Monday.
The 49ers fired rookie coach Jim Tomsula on Sunday. San Francisco went 5-11 in Tomsula's lone season as head coach.
Communication issues with players and management appear to have been part of the reason the Eagles fired Kelly. Owner Jeffrey Lurie has made it clear what qualities he wants the next coach to have: "Looking for somebody who interacts very well and communicates clearly with everybody he works with and comes in touch with," he said.
When the 49ers parted ways with coach Jim Harbaugh at the end of the 2014 season, clashes with management, particularly general manager Trent Baalke, were often cited for the split.
Information from ESPN's Paul Gutierrez was used in this report.
Is Chip Kelly a good fit in San Francisco?
ESPN NFL Insider Phil Savage discusses whether Chip Kelly would fit in as coach of the 49ers, as well as whether his style of offense would gel with Colin Kaepernick at quarterback.