In 2001, funds in the amount of $17 million were approved by the tri-town area in an effort to completely renovate the school as well as construct a new gymnasium and additional classroom space.

During the renovation, the much beloved Star Wars mural that had covered the main wall of the old cafeteria had to be dismantled.

Winnisquam tied for the lowest rank of any NHIAA finalist during the fall 2007 season (11th, also achieved by Portsmouth field hockey) and earned the school's soccer program its first championship appearance in 44 years.

Its best year on record was in 2015 when the team placed 3rd at the state tournament led by seniors Richie Mills, Billy Chavanelle, and Christian Duquette.

The Bears went undefeated in the 2018 season and beat Franklin in the championship, becoming Division IV state champions and winning their first title.

Winnisquam Regional High School also has a tremendous amount of participation in its music department.