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1946–2010

Founded in 1946 as Wahingdoh Sports Club, the club based in Shillong, won numerous titles. However, with changing times and professionalisation, the amateur club began to face some amount of difficulty competing with younger clubs and it was then, that the decline began.

In 2007, Wahingdoh Sports Club was almost relegated to the 2nd Division League and as a result of inconsistent performance, the Wahingdoh community felt the need for a younger and more innovative approach. In 2008, the club turned professional when it merged with Royal Football Club before being renamed Royal Wahingdoh FC under the able leadership of the club's owner Dominic Sutnga Tariang. With the club witnessing several dramatic changes, a new chapter was in the making and in the very same year, the club bounced back to claim Third spot in the 2nd Division Regional League, a sign that brought hope for a brighter future. In the First Division 2009 season, they created a record by winning all their games besides scoring 52 goals en route to lifting the title and along with it, an entry into the top tier of Meghalaya football, the Shillong Premier League.

2010–2015

Royal Wahingdoh FC was Shillong's one of the two most popular clubs. In the 2010 season, they lifted the Shillong Premier League – in their debut season. In 2011, Carlton Chapman was appointed as new head coach, and they lifted the trophy in 2011 and 2012. In 2011, the club signed Liberian international Bekay Bewar who helped the side gaining promotion to the I-League, and was retained by the Shillong based side for there season. The same year, they lifted Bordoloi Trophy.

In 2014, Royal Wahingdoh achieved their biggest success after winning the I-League 2nd Division, then second tier of indian football league system. They qualified for the 2014 I-League 2nd Division final round and finished on top spot with 18 points in 8 matches after defeating Bhawanipore in the final match. Thus they were declared as the debutants of the 2014–15 I-League season. They have also participated in the 2014 Federation Cup.

Santosh Kashyap was appointed the head coach for newly promoted Royal Wahingdoh before the start of the 2014–15 I-League. They signed Trinidad and Tobago international Densill Theobald as marquee player, who represented his nation at the 2006 FIFA World Cup. The club also appeared in the 2014–15 Federation Cup and defeated Mumbai 2–1 in the tournament opener. They lost 2–1, narrowly, to Sporting Goa on 4 January 2015. Royal Wahingdoh began their regular league season on 18 January in a match against Shillong Lajong, which was the first ever Shillong Derby in the I-league, in their 2–1 win, before facing Salgaocar next. They later drew 1–1 with Kalyani Bharat on 21 March 2015. they later defeated Pune in a 2–0 win in Shillong on 29 March 2015. The club then also defeated East Bengal on 31 March 2015, by 1–0. On 3 May, club's striker Jackichand Singh assisted teammate Satiyasen Singh thrice the hat-trick against Salgaocar in their 4–2 win. At the end of the 2014–15 season, Jackichand Singh was awarded best player of the season award. Under his coaching, Royal Wahingdoh stun eventual champions Mohun Bagan by 3–2 margin, and ended the season in third position with 30 points in 20 league matches.