The Atlanta Falcons selected Trufant in the first round (22nd overall) of the 2013 NFL Draft. He was the third cornerback selected in 2013, behind Alabama's Dee Milliner (9th overall) and Houston's D. J. Hayden (12th overall), and was also the first of two cornerbacks the Falcons selected, along with second round pick Robert Alford (60th overall).
On July 24, 2013, the Atlanta Falcons signed Trufant to a four-year, $8.16 million contract that includes $6.94 million guaranteed and a signing bonus of $4.31 million.
He made his professional regular season debut and first career start in the Atlanta Falcons' season-opener at the New Orleans Saints and made five combined tackles and a pass deflection in a 23–17 loss. In Week 7, Trufant recorded a season-high seven combined tackles and broke up a pass during a 31–23 victory against the Tampa Bay Buccaneers. On November 3, 2013, Trufant recorded five combined tackles, a pass deflection, and his first career interception off a pass by quarterback Cam Newton in the Falcons' 34–10 loss at the Carolina Panthers. On December 15, 2013, Trufant tied his season-high with seven combined tackles, two pass deflections, and intercepted a pass by quarterback Kirk Cousins in their 27–26 victory against the Washington Redskins. He finished his rookie season in 2013 with a career-high 70 combined tackles (55 solo), a career-high 17 pass deflections, two interceptions, one forced fumble, and two fumble recoveries in 16 games and 16 starts. He exceeded expectations, being ranked eighth out of all cornerbacks in the league by Pro Football Focus and allowed a 53.% completion percentage and a quarterback rating of 75.2 to opposing quarterbacks in pass coverage.