Founded on 1 April 1989, Pinheiro played in the 1990, 1991, 1992 and 1993 editions of Campeonato Maranhense before going into inactivity.

The club returned to an active status only in 2016, playing in the Maranhense Segunda Divisão, where they lost the title and the promotion to Americano.

After finishing in the last position in the 2017 second division, Pinheiro won promotion as champions in 2018, finishing the tournament undefeated.

[2] The club remained in the first division in the following years, after finishing fifth and six in 2019 and 2020, respectively.

In the 2021 edition of the Maranhense, Pinheiro reached the semifinals and were knocked out on penalties by eventual champions Sampaio Corrêa, finishing third in the competition.