After returning from the Spalding tour, Hanlon joined the Pittsburgh Alleghenys and took over as a player-manager in the second half of the season.
 The Alleghenys had compiled a 35-53 record and were languishing near the basement of the National League before Hanlon took over as manager.
 In the last part of the season, Hanlon led the team to a 26-18 record.
As a player, Hanlon compiled a .239 batting average (.326 on-base percentage), scored 81 runs, and stole 53 bases during the 1889 season.

In late 1889, Hanlon was one of the early supporters and organizers of the new Players' League.
 He served as player-manager for the Pittsburgh Burghers during the 1890 season.
In Hanlon's first full season as a manager, his team compiled a 60-68 record and finished in sixth place in the Players' League.
 Hanlon put in a solid performance as a player in 1890, posting a .278 batting average and a career high .389 on-base percentage fueled by a career high 80 bases on balls.
 He also led the Players' League with 291 outfield putouts, posted a 2.59 range factor (3rd highest among the league's outfielders), and ranked fourth in the league with 65 stolen bases.

The Players' League folded after one season, though Hanlon was credited with working harder than anyone else to make the league a success.
One account published in late 1890 stated: "I want to say, gentlemen, that you can talk of the loyalty of a Ward, a Ewing, a Keefe and so on, but give me Ned Hanlon above everybody else.
He stands to-day as the hero of the Players' League.
He is the only ball player in that League who has held to the contract he signed.
Not a penny has he received for his work this season, although he has played better ball than ever before."

Hanlon returned to the Alleghenys as player-manager in 1891.
Prior the 1891 season, Hanlon was involved in an incident that led to the Pittsburgh team acquiring the name "Pirates."
 After the collapse of the Players' League, Hanlon traveled to Pennsylvania's Presque Isle Peninsula in the dead of winter to sign second baseman, Louis Bierbauer.
 Alfred Spink, the founder of The Sporting News, wrote about the incident in 1910 for a journal called The Pirates Reader.
According to Spink, Hanlon crossed the ice on the harbor during a snow storm, finally reached Bierbauer's home and got him to sign a contract with the Alleghenys.
The Philadelphia Athletics of the American Association, objected to Bierbauer's signing and stated that he should return to Philadelphia, since that was the team that employed him before his defection to the Players' League.
An official for the American Association called Hanlon's act in signing Bierbauer to be "piratical."
The Alleghenies contended that because "the American Association did not reserve Bierbauer, he was a free agent".
An arbitrator agreed, and soon players and fans alike were calling the team the "Pittsburgh Pirates."

The 1891 season was Hanlon's last as a full-time player.
 At age 34, he compiled a .266 batting average and .341 on-base percentage, scored 87 runs, and stole 54 bases.
 He was also manager of the Alleghenys for most of the 1891 season, during which time the team compiled a record of 31–47.
After returning from the Spalding tour, Hanlon joined the Pittsburgh Alleghenys and took over as a player-manager in the second half of the season.  The Alleghenys had compiled a 35-53 record and were languishing near the basement of the National League before Hanlon took over as manager.  In the last part of the season, Hanlon led the team to a 26-18 record. As a player, Hanlon compiled a .239 batting average (.326 on-base percentage), scored 81 runs, and stole 53 bases during the 1889 season.
In late 1889, Hanlon was one of the early supporters and organizers of the new Players' League.  He served as player-manager for the Pittsburgh Burghers during the 1890 season. In Hanlon's first full season as a manager, his team compiled a 60-68 record and finished in sixth place in the Players' League.  Hanlon put in a solid performance as a player in 1890, posting a .278 batting average and a career high .389 on-base percentage fueled by a career high 80 bases on balls.  He also led the Players' League with 291 outfield putouts, posted a 2.59 range factor (3rd highest among the league's outfielders), and ranked fourth in the league with 65 stolen bases.
The Players' League folded after one season, though Hanlon was credited with working harder than anyone else to make the league a success. One account published in late 1890 stated: "I want to say, gentlemen, that you can talk of the loyalty of a Ward, a Ewing, a Keefe and so on, but give me Ned Hanlon above everybody else. He stands to-day as the hero of the Players' League. He is the only ball player in that League who has held to the contract he signed. Not a penny has he received for his work this season, although he has played better ball than ever before."
Hanlon returned to the Alleghenys as player-manager in 1891. Prior the 1891 season, Hanlon was involved in an incident that led to the Pittsburgh team acquiring the name "Pirates."  After the collapse of the Players' League, Hanlon traveled to Pennsylvania's Presque Isle Peninsula in the dead of winter to sign second baseman, Louis Bierbauer.  Alfred Spink, the founder of The Sporting News, wrote about the incident in 1910 for a journal called The Pirates Reader. According to Spink, Hanlon crossed the ice on the harbor during a snow storm, finally reached Bierbauer's home and got him to sign a contract with the Alleghenys. The Philadelphia Athletics of the American Association, objected to Bierbauer's signing and stated that he should return to Philadelphia, since that was the team that employed him before his defection to the Players' League. An official for the American Association called Hanlon's act in signing Bierbauer to be "piratical." The Alleghenies contended that because "the American Association did not reserve Bierbauer, he was a free agent". An arbitrator agreed, and soon players and fans alike were calling the team the "Pittsburgh Pirates."
The 1891 season was Hanlon's last as a full-time player.  At age 34, he compiled a .266 batting average and .341 on-base percentage, scored 87 runs, and stole 54 bases.  He was also manager of the Alleghenys for most of the 1891 season, during which time the team compiled a record of 31–47.
Ned Hanlon (baseball)