In July of that year, the New York Giants purchased his contract from Norfolk for $1,500.. Between July and December of Mathewson appeared in six games for the Giants. He started one of those games and compiled a 0-3 record. Displeased with his performance, the Giants returned him to Norfolk and demanded their money back. Later that month, the Cincinnati Reds drafted Mathewson in the Rule 5 draft.
On December 15, 1900, the Reds traded him to the Giants in exchange for Amos Rusie.
During his 17-year career, Mathewson won 373 games and lost 188. His career ERA of 2.13 and 79 career shutouts are amongst the best all-time for pitchers. Employing a good fastball, outstanding control, and, especially, a new pitch he termed the "fadeaway" (later known in baseball as the "screwball"), which he learned from teammate Dave Williams in , Mathewson recorded 2,502 career strikeouts against 844 walks. He is famous for his pitching duels with Mordecai "Three Finger" Brown, who won most of the duels against Mathewson.
Mathewson's Giants won the 1905 World Series over the Philadelphia Athletics. Mathewson was the starting pitcher in Game 1, and pitched a 4-hit shutout for the victory. Three days later, with the series tied 1-1, he pitched another 4-hit shutout. Then, two days later in Game 5, he threw a 6-hit shutout to clinch the series for the Giants. In a span of only six days, Mathewson had pitched three complete games without allowing a run.
The 1905 World Series capped an impressive year for Mathewson as he had already won the National League Triple Crown for pitchers, and threw the second no-hitter of his career. He claimed the Triple Crown again in , and by the time he left the Giants, the team had captured four more National League pennants, in addition to the aforementioned appearance in the World Series.
As noted in The National League Story (1961) by Lee Allen, Matty never pitched on Sunday. The impact of this on the Giants was minimized, since, in the eight-team National league, only the Chicago Cubs (Illinois), Cincinnati Reds (Ohio), and St. Louis Cardinals (Missouri), played home games in states that allowed professional sports on Sunday.
Along with his brother Henry Mathewson, he holds the major league record for combined wins by brothers playing for the same team: Christy 373, Henry 0.
Mathewson and Brown wrapped their respective careers by squaring off on September 4, 1916. The game was billed as the final meeting between the two old baseball warriors. The high-scoring game was a win for Mathewson's Reds over Brown's Cubs.
Two years later, he died in Saranac Lake, New York. He is buried at Lewisburg Cemetery in Lewisburg, Pennsylvania. Members of the Pittsburgh Pirates and the Washington Senators wore black armbands during the 1925 World Series. Mathewson had died on the day the Series began.
Mathewson is mentioned in the poem "Lineup for Yesterday" by Ogden Nash:
| G | AB | H | 2B | 3B | HR | R | RBI | BB | SO | AVG | OBP | SLG | OPS |
| 646 | 1,684 | 362 | 50 | 12 | 7 | 151 | 165 | 116 | 74 | .215 | .272 | .271 | 61 |
| W | L | WP | GP | GS | CG | Sh | SV | IP | BB | SO | ERA | WHIP |
| 373 | 188 | .665 | 635 | 551 | 434 | 79 | 28 | 4780.7 | 844 | 2,502 | 2.13 | 1.059 |
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