Click succeeds Jeff Luhnow, who along with manager AJ Hinch was suspended by Major League Baseball last month in the wake of a sign-stealing scam and then fired by the Astros.
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Houston, coming off a Game 7 loss to Washington in the World Series, hired Dusty Baker last week as manager.
Astros owner Jim Crane announced the addition of Click, who spent the last three seasons as the Rays' vice president of baseball operations. The 42-year-old Click had been with Tampa Bay for the last 14 seasons.
"I am excited to join the Astros family," Click said in a statement. "The Astros are a progressive and innovative organization with a deeply talented group in the front office."
The Rays beat Oakland in the AL wild-card game and lost to Houston in the decisive Game 5 of the Division Series. Tampa Bay senior vice president of baseball operations Chaim Bloom was hired as chief baseball officer by the Boston Red Sox in late October.
"The departure of another talented, senior Rays executive is difficult," Tampa Bay owner Stuart Sternberg said in a statement. "That difficulty is compounded by the timing of the departure, only days from the opening of spring training."
"A large number of former Rays staffers now populate senior team positions across the league. Most recently, two of the past three World Series winning teams, against whom we compete directly, have reached beyond their organizations and into our ranks to fill their top baseball operations positions," he said. "We have great organizational leadership, strong faith in our ability to regenerate, and we have supreme confidence in the men and women who will be stepping up into their newfound opportunities and responsibilities. That is the Rays way. It is who we are, it is what we do."
Click was to be formally introduced by the Astros at a news conference on Tuesday at Minute Maid Park.
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"James has had an impressive career," Crane said in a statement. "He is a respected leader who has progressed in this game across all aspects of baseball operations and he has built great relationships with both front office and clubhouse personnel."
Click graduated from Yale and wrote for analytics website Baseball Prospectus for several years before being hired by the Rays.
Click was involved in guiding and overseeing all aspects of the baseball operations department. His areas of focus were research and development, strategic planning and innovation.
Luhnow and Hinch were suspended for a year by Commissioner Rob Manfred on Jan. 13 after he found the Astros used electronics to illicitly steal signs during their run to the 2017 World Series championship and again in the 2018 season. Crane announced hours later that Luhnow and Hinch were fired.
The Astros also were fined $5 million, the maximum allowed under the Major League Constitution, and forfeited their next two first- and second-round amateur draft picks.
Álex Cora, the bench coach for the Astros in 2017 and the manager who guided the Red Sox to the 2018 World Series title, recently parted with Boston. Carlos Beltrán, singled out for his role in the cheating scheme while playing for the 2017 Astros, was let go as manager of the New York Mets last month before working his first game.