Coughlin, 69, and Baalke have a connection through Bill Parcells and Coughlin will be the sixth candidate to receive an interview with the Niners, who fired Jim Tomsula after one 5-11 season on Jan. 3.
Niners CEO Jed York is in Houston for the NFL owners relocation meetings.
Coughlin resigned after 12 years as the Giants coach and two Super Bowl victories last week, and because he resigned with one year left on his contract, rather than retiring or being fired, the 49ers had to request permission from the Giants to interview him. He interviewed with the Philadelphia Eagles on Monday night.
Since 1991, Coughlin has been a head coach at Boston College, or with the Jacksonville Jaguars and the Giants every year but two. He has an NFL record of 170-150 in the regular season, 12-7 in the playoffs.
Others to have interviewed with the Niners: Buffalo Bills assistant head coach/running back coach Anthony Lynn, former Eagles coach Chip Kelly, Cleveland Browns offensive coordinator John DeFilippo, Tampa Bay Buccaneers offensive coordinator Dirk Koetter and Cincinnati Bengals offensive coordinator Hue Jackson, who has also drawn strong interest from the Browns as well as the Giants.