In December 1954, Pajaczkowski and Geary were signed by the Calgary Stampeders of the Western Interprovincial Football Union (WIFU).[6] Pajaczkowski made the roster in his first year and appeared in 12 games for the 1955 Stampeders at tackle and defensive end, mainly playing on kickoff teams.[4][7] In 1956, his position was changed to guard by coach Jack Hennemier.[8] Although initially reluctant to change, it was at this position that he became one of the all-time greats of Canadian football.[8] In his first year at guard, Pajaczkowski earned a starting role and appeared in all 16 games as the Stampeders finished 4–12.[9][10] In addition to playing at guard, he was also used by Calgary as a kicking specialist.[10]
Pajaczkowski signed a contract extension in March 1957.[10] Coach Otis Douglas called him one of Calgary's best Canadian prospects.[10] He continued as starter in 1957, playing in every game as the Stampeders finished third place in the conference with a record of 6–10.[11] On special teams, he made eight kickoffs for 391 yards, a 48.9 average.[4]
The Vancouver Sun reported in July 1958 that Pajaczkowski was "not far behind" teammate Harry Langford as the league's most outstanding guard.[12] He was re-signed that year and played in every game, helping Calgary to a record of 6–9–1 and a fourth-place conference finish.[13][14] After playing in 14 games in 1959, Pajaczkowski was named the team's best lineman by a fan vote.[15]
Due to pronunciation difficulties, announcer Jack Wells refused to mention Pajaczkowski's name (pronounced pa-jə-KOW-skee) in all of the Calgary game broadcasts from 1955 to 1959.[2][16]
Pajaczkowski appeared in 16 games in 1960, helping Calgary reach the second round of the WIFU playoffs.[17] In addition to being their starting guard, he was the team's backup kickoff specialist that year, making 27 kickoffs for 1495 yards, a 55.4 yard average.[17] He was the Stampeders' nominee for the Schenley Most Outstanding Canadian Award and was the runner-up for the honor.[8]
In 1961, Pajaczkowski made 51 kickoffs for 2845 yards, an average of 55.8 yards per kick, and started all 16 games at guard, being named to the Western Football Conference All-Star team and earning the Most Outstanding Canadian Award.[18][19]
The following year, Pajaczkowski was named for the first time of his career to the CFL All-Star team.[20] He was one of six Stampeders to be given that honor.[20] In 1963, he was named all-star for the second consecutive season.[21][22] He was named all-star for a third time in 1964 and in 1965 earned his fourth-straight all-star honor.[23][24]
On May 19, 1966, Pajaczkowski was traded to the Montreal Alouettes.[25] He played in all 14 games in his first year with the team.[26] After a knee injury in a 1967 practice, he changed his position from right guard to right tackle.[7] In a game against his former team, Calgary, Pajaczkowski was benched for the first time in his career.[7] He announced his retirement in June 1968.[27]