Prior to the start of the 2006 college football season, Quinn was featured in a regional cover on the August 22, 2006 issue of "Sports Illustrated"'s 2006 College Football Preview issue along with then-teammates Tom Zbikowski and Travis Thomas with the caption "Notre Dame: The Battle For No. 1." Quinn finished the season with 3,426 yards on 289 completions out of 467 attempts for a completion percentage of 61.9% and 7.34 yards per attempt. He threw 37 touchdowns to only 7 interceptions, and was sacked 31 times. Quinn finished the regular season with a passing efficiency rating of 146.65, which ranked him 18th in the country. Notre Dame invited to the 2007 Sugar Bowl on January 3, 2007, where they played LSU. Quinn was held to 148 passing yards. Quinn threw two touchdown passes, both in the first half, and LSU held Notre Dame scoreless through the second half of the game to defeat the Fighting Irish 41–14.