He has previously played in MLB for the Tampa Bay Rays, Seattle Mariners, Oakland Athletics, San Diego Padres, and Minnesota Twins.

Pagán spent 2016 with the Jackson Generals and Tacoma Rainiers, compiling a combined 5–3 record and 2.49 ERA in 65 innings pitched out of the bullpen.

[3] On November 15, 2017, Pagán was traded to the Oakland Athletics, along with Alexander Campos, in exchange for Ryon Healy.

On February 8, 2020, the Rays traded Pagán to the San Diego Padres in exchange for Manuel Margot and Logan Driscoll.

[9] The Padres traded Pagán, Chris Paddack and a player to be named later to the Minnesota Twins for Taylor Rogers, Brent Rooker, and cash considerations on April 7, 2022.

[11] The Twins and Pagán avoided salary arbitration by agreeing to a one year, $3.5 million contract on January 13, 2023.

He pitched two scoreless innings and helped Puerto Rico earn a silver medal in the 2017 World Baseball Classic.

[17] Pagán pitched one scoreless inning for Puerto Rico during the 2023 World Baseball Classic, helping his team reach the quarterfinals.