The NFC champions acquired the pick from the Green Bay Packers on Friday, giving up the 61st choice in the second round and a sixth-round pick at No. 173.
San Francisco lost Delanie Walker, the backup to Vernon Davis, to the Titans last month in free agency.
The 6-foot-4, 262-pound McDonald caught 119 passes for 1,504 yards and 15 touchdowns in college.
McDonald says special teams wasn’t emphasized for him at Rice considering his high repetitions, but he is willing to take on whatever task the 49ers ask of him. McDonald says he is “extremely underdeveloped” but plans to use his raw talent.