The club was founded in 1979 as Avtomobilist by the workers of the Motor Depot 13 in
Narva. In 1984, the club was promoted to the Estonian SSR Championship, but was relegated at the end of the
season. The club returned to the top division in 1987, but was relegated again after finishing the
season last. In 1989, the club changed its name to Autobaas and returned to the top division once again. In 1992, the club changed the name to Narva Trans and became founding members of the new
Meistriliiga, finishing the
inaugural season in seventh place. The club earned their first medals after reaching the
1993–94 Estonian Cup final, finishing as runners-up. One year later, Narva Trans earned their first league medals by finishing the
1994–95 league season in third place. The club made their European debut in the
1996 UEFA Intertoto Cup. in 2011 On 24 May 2001, Narva Trans lifted their first trophy by defeating
Flora 1–0 in the
2000–01 Estonian Cup final. Narva experienced their most successful period from 2005 to 2011, as the club first came third in the
2005 league season and finished as runners-up in
2006 with club record 83 points, their best league finish to this date. The team won back-to-back
Estonian Supercups in 2007 and 2008 by defeating
Levadia in both of the finals. Narva Trans finished third for four consecutive seasons in
2008,
2009,
2010 and
2011. In the years that followed, financial competition with the capital city clubs grew more difficult, and Narva Trans gradually transitioned into a mid-table club. Since then, the team has occasionally been referred to as "cup specialists" in recognition of their strong performances in the Estonian Cup competition. The club won their second Estonian Cup trophy in the
2018–19 season, defeating
Nõmme Kalju 2–1 after extra time in the final. In 2023, Narva Trans won their third Estonian Cup by defeating
FC Flora 2–1 in the
2022–23 final. == Crest and colours ==