Re-established in 1992 as Viljandi JK, Tulevik are a founding member of the Meistriliiga. The club finished the 1992–93 season last and were relegated to the Esiliiga. Tulevik returned to the Meistriliiga in 1997, when another Flora affiliated club Lelle moved to Viljandi. Tulevik finished the 1999 Meistriliiga season as runners-up and also played in two successive Estonian Cup finals in 1999 and 2000, losing to Levadia 2–3 and 0–2 respectively.
Since 2011 Tulevik has once again become an independent club and was relegated to the II liiga, while FC Viljandi replaced Tulevik in the Meistriliiga. Tulevik finished the 2014 Esiliiga season in 5th place and defeated Lokomotiv 1–1 on aggregate on away goal in the promotion play-offs, thus earning promotion to the Meistriliiga. Tulevik's stay in the top division proved short-lived, as the club finished the 2015 season in last place and was relegated. The club won the 2016 Esiliiga, and were once again promoted to the Meistriliiga.