Wojciechowicz was selected by the Detroit Lions in the first round of the 1938 NFL Draft and played for the Lions from 1938 to 1946. He was selected as a first-team All-NFL player in 1939 and 1944. In 1946, he was released by the Lions and then sold to the Philadelphia Eagles, for whom he played from 1946 to 1950. He won two NFL championships with the Eagles, in 1948 and 1949.
Fordham coach Jim Crowley called Wojciechowicz "one of the great defensive centers" and noted that he "seldom made a bad pass from center." He made a name for himself in the annual rivalry games with Pittsburgh, resulting in three consecutive scoreless ties. The final tie was the only blemish on the record of the 1937 Pitt team that won the national championship in the AP Poll. Wojciechowicz later cited the Pitt games as his three biggest thrills in football, saying, "Pitt had the dream backfield, with all-America Marshall Goldberg, and we had the dream line. It was a stalemate for three years. Those three games proved what football is all about."
Wojciechowicz was selected by the Detroit Lions in the first round, sixth overall pick, of the 1938 NFL Draft. He signed with the Lions in July 1938. For nine years, Wojciechowicz was a fixture in the Lions' lineup, a 60-minute player who played at center on offense and linebacker on defense. He was selected as a first-team All-NFL player in 1939 and 1944 and had seven interceptions in 1944, a Lions single-season record at the time. Between 1938 and 1946, he appeared in 86 games for the Lions, 61 of them as a starter. The Pro Football Hall of Fame, in its biography of Wojciechowicz, states: "On the field, . . . he was all business, one of the last of the 'iron men' of football, a center on offense and a sure-tackling linebacker with unusually good range, on defense." In October 1946, after the Lions lost their season opener, Detroit coach Gus Dorais released four linemen, including Wojciechowicz. Wojciechowicz announced at the time that he would return to his business in New Jersey and added, "This day had to come, and I can't say I'm disappointed that it happened now."
Two days after the Lions announced his release, the Eagles purchased the Lions' rights to Wojciechowicz for an undisclosed sum. He appeared in seven games for the Eagles, only one as a starter, during the 1946 season.
In 1947, he became the Eagles' starting center, appearing in all 12 games for the club, 11 as a starter. The 1947 Eagles compiled an 8–4 record, finished in first place in the NFL East, but lost to the Cardinals in the 1947 NFL Championship Game.
He was considered past his prime when he joined the Eagles, but head coach Greasy Neale used him principally as a linebacker, and he responded with quality defensive play. Teammate Jack Hinkle called Wojciechowicz the "toughest guy" on the Eagles' championship teams and added, "He looked like a big, shaggy dog. A sad-eyed St. Bernard. But he'd rip your head off."
In his final NFL season, Wojciechowicz appeared in nine games, none as a starter, and saw only limited action. In December 1950, he announced that he was retiring as a player.
Wojciechowicz was married to Katherine Mallen, and they had three sons and a daughter. For many years after retiring from the NFL, he lived in Wanamassa, New Jersey, and worked as a real estate appraiser and broker.
Wojciechowicz was also one of the founders of the NFL Alumni Association, established to negotiate with the owners for the creation of a pension plan to benefit the game's early players, and was elected as its president in 1968. His son recalled: "He worked hard to establish the indigent players' fund and establish pensions."
After retiring from football, Wojciechowicz received numerous honors including the following:
In 1968, he was inducted into the Pro Football Hall of Fame. At the time, Bill Daley wrote in The New York Times: "Fewer than a dozen men had the durability and continuing excellence to survive the rigors of smashing play for a longer period of time."