Marichal entered the major leagues in 1960 with the San Francisco Giants, for whom he made an immediate impression by going 6-2 in eleven starts with a 2.66 ERA. He improved his victory totals to thirteen and eighteen over the following two seasons respectively before finally cracking the twenty-victory plateau in 1963, when he went 25-8 with 248 strikeouts and a 2.41 ERA. Marichal enjoyed similar success through the 1969 season, posting over 20 victories in every season except 1967 and never posting an ERA higher than 2.76. He led the league in victories in 1963 and 1968 when he won 26 games.

Probably the most notorious incident in Marichal's career occurred on August 22, 1965. Batting against Sandy Koufax of the hated Los Angeles Dodgers, Marichal felt Dodger catcher John Roseboro's return throws had flown too close to his head. Words were exchanged and, as Roseboro rose to continue the argument, Marichal began to beat his unprotected head with the bat. The benches cleared into a fourteen minute brawl, while Giant captain Willie Mays escorted the bleeding Roseboro (who would require fourteen stitches) back to the clubhouse. Marichal was ejected, suspended for nine days and fined $1,750. Roseboro filed a lawsuit, but eventually settled out of court, supposedly for $2,000. Marichal and Roseboro would eventually go on to become close friends, reconciling any personal animosity and even autographing photographs of the brawl.

Marichal's career stumbled in 1970, when he only posted 12 wins and his ERA shot up to 4.12, before straightening itself out with a stellar 1971 season in which he won 18 games and his ERA dropped below 3. It was his final great season, however, as he posted 6-16 and 11-15 records in 1972 and 1973 respectively. He played briefly with the Boston Red Sox in 1974 and the Los Angeles Dodgers in 1975 before retiring. He finished his career with 243 victories, 142 losses, 244 complete games, 2303 strikeouts and a 2.89 ERA over 3507.3 innings pitched. His teams appeared in two post-seasons (in 1962 and 1971) but were not victorious in either series. Between 1962 and 1971, The Giants averaged 90 wins per season, and Marichal averaged 20 wins per year.

Marichal pitched a no-hitter on June 15, 1963 and was named to nine All-Star teams, being selected MVP in the 1965 game. He pitched in those games and went 2-0 and a 0.50 ERA.

Juan Marichal was selected to the Baseball Hall of Fame in 1983. His uniform number 27 has been retired by the Giants. In 1990, Marichal, who was working as a broadcaster for Spanish radio, was on hand to see his son-in-law Jose Rijo win the World Series Most Valuable Player Award.

In 1999, he ranked #71 on The Sporting News' list of the 100 Greatest Baseball Players, and was a finalist for the Major League Baseball All-Century Team. He was honored before a game between the Giants and Athletics with a statue outside SBC Park in 2005, and was named one of the three starting pitchers on Major League Baseball's Latino Legends Team.