The franchise has lost 100+ games twice, both seasons when they were known as the Highlanders.
1) 1908: record was 51-103
2) 1912: record was 50-102
Since the franchise changed the name to Yankees in 1913, the most games the team has lost in a season is 95 in 1990.
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The Phillies 10,000th loss came on July 15, 2007 when they lost to the St. Louis Cardinals, 10-2, in front of 44,872 at Citizens Bank Park.