A 3-over 75 on Wednesday left him in a tie for 55th and 11 strokes behind leader Chip Sullivan. The top-23 and ties will advance from the Key Biscayne, Fla. qualifying site.
He is, however, just five strokes off the pace of being included in the top 23 with two days remaining.
Compton, who received his second heart transplant just five months ago, applied for and was granted the use of a cart from the PGA Tour during Q-School.
The Miami native was diagnosed at age 9 with cardiomyopathy, a condition that threatens the body's ability to pump blood to the heart.