Wilson did not receive an invitation to the NFL Scouting Combine. He was invited to the Super Regional Combine in Detroit, Michigan, but declined the invitation. On March 30, 2012, he participated at Illinois' pro day and performed all of the combine and positional drills. During the draft process, Wilson attended private visits with multiple teams, including the Tampa Bay Buccaneers, Houston Texans, Arizona Cardinals, Atlanta Falcons, Indianapolis Colts, Baltimore Ravens, and San Diego Chargers. At the conclusion of the pre-draft process, Wilson was projected to be a sixth or seventh round pick by the majority of NFL draft experts and scouts. He was ranked the ninth best free safety prospect in the draft and was ranked the 24th best safety in the draft by ESPN Scouts inc.
The New England Patriots selected Wilson in the second round (48th overall) of the 2012 NFL Draft. Wilson was the third safety drafted in 2012, behind Mark Barron and Harrison Smith. The Patriots' selection of Wilson was immediately met with criticism as he was a virtually unknown prospect. Many analysts questioned the selection and labeled it a reach by head coach Bill Belichick. NFL draft analyst Mel Kiper did not have any notes on Wilson due to low draft status.
On May 12, 2012, the New England Patriots signed Wilson to a fully guaranteed four-year, $4.21 million contract that includes a signing bonus of $1.50 million.
He made his professional regular season debut in the New England Patriots' season-opener at the Tennessee Titans and recorded four combined tackles, two pass deflections, and made his first career interception off a pass by Jake Locker in their 34–13 victory. Wilson made his first career tackle on Chris Johnson in the second quarter. On October 7, 2012, Wilson earned his first career start in place of Steve Gregory who sustained a hip injury. He collected a season-high ten combined tackles (five solo) during their 31–21 victory against the Denver Broncos in Week 5. In Week 8, he recorded three combined tackles, a pass deflection, and returned an interception by Case Keenum for a 45-yard gain during a 45–7 victory against the St. Louis Rams at Wembley Stadium. He finished his rookie season with 41 total tackles (28 solo), six pass deflections, and four interceptions in 16 games and four starts. Wilson played in 464 snaps on defense (42.3%) and played 238 snaps on special teams (48.7%).