Shillong Lajong Lyngdoh signed for
Shillong Lajong in 2011 from
Rangdajied United, who were then known as
Ar-Hima, for whom he was the captain in the last season. He finished as the top scorer for Lajong during the
2011-12 I-League scoring 4 times. He then went on to make 23
I-League appearances for Lajong during the
2012-13 I-League season.
Rangdajied United After spending 2 years with
Shillong Lajong, Lyngdoh re-signed for
Rangdajied United and made his debut in the
I-League on 22 September 2013 against
Prayag United at the
Salt Lake Stadium, playing the full match as Rangdajied lost 0–2. He made 19 I-League appearances for Rangdajied.
Bengaluru FC 2014–15 In July 2014 Lyngdoh signed a one-year deal with
I-League winners Bengaluru FC. Lyngdoh scored his first goal for Bengaluru during the
2014 Durand Cup, in a game against
Mohammedan. Eugene then scored his second goal in the
2014–15 Federation Cup semi-final against
Sporting Goa in a 3–0 win. Eugene kept up his high level of performances and scored Bengaluru FC's first goal of the
2014-15 I-League in a disappointing 1–3 defeat at home to
Pune, with an outstanding finish. He scored again, this time in the 4th round of the season against
Royal Wahingdoh in a 4–0 away win in Shillong. Eugene then created history by scoring
Bengaluru FC's first ever goal in Asian continental club competition in an
AFC Champions League qualifier against
Johor Darul Ta'zim of Malaysia in a 2–1 loss, directly from a corner. By scoring against Johor, he became the first player from an I-League club to score in all four club competitions in the season. He assisted club captain
Sunil Chhetri during an away game at
Mohun Bagan for Bengaluru's opener, but couldn't prevent his team from going down 4–1 at Kolkata. Lyngdoh assisted
Josh Walker in a 4–1 win against
Sporting Goa on 31 March 2015 with a free-kick into the box, which was headed in for the first goal by the latter. He continued his fine form with another assist from a free-kick into the box for
Shankar Sampingiraj to head home in a thrilling 3–3 draw at home to
Royal Wahingdoh on 3 April 2015. He assisted Sampingiraj again, this time against
Pune on 21 April 2015 with a cross from the left before scoring with a spectacular first time shot from outside the box, and assisting
C.K. Vineeth on 24 April 2015 against
Bharat FC. Lyngdoh augmented his statistics for the season with an assist from a free-kick into the box for Sean Rooney to head home against
Shillong Lajong in a 1–1 away draw. On 17 May 2015, Lyngdoh assisted once and scored once against
Salgaocar in a crucial 3–1 win for his team. Lyngdoh was involved in the last goal his team scored of the season, in the final round against
Mohun Bagan, in a title-deciding match, assisting
John Johnson from a corner, but couldn't help his team win in the game that ended 1–1, and thus losing out on the title. Lyngdoh was rewarded for an outstanding season, where he made 33 appearances in all competitions, scoring 9 times and assisting 16 times, when he was named Bengaluru FC Fan's Player of the Year and Player's Player of the Year, as well as being named the 2014–15 I-league Midfielder of the Season. Lyngdoh signed a 2-year extension to his contract that would keep him at Bengaluru FC until the end of 2016–17 season on 4 June 2015.
FC Pune City (loan) Lyngdoh was signed by
Indian Super League club
Pune City on 10 July 2015 in the player drafts for Rs. 1.05 crore (US$214,431) for the
2015 Indian Super League. Pune City's manager
David Platt praised Eugeneson for his technical ability and explained why the Pune-based franchise paid very high for his services. On 28 September 2015, he was named the "Football Player Association of India"s (FPAI) player of the year. Lyngdoh scored his first goal of the Indian Super League against
FC Goa in his 5th game of the season, from a header in a 1–1 draw at Goa. He scored again on his 7th game of the season against
FC Goa from a
Didier Zokora pass. On 20 December 2015, Euegenson was voted by the coaches in the I-League as the best among the Indians, thus winning the "2015 AIFF Player of the Year".
ATK Lyngdoh was picked up by
ATK in the draft for the
2017–18 Indian Super League. Most of his time in the club was on the bench due to injury. The club decided to make a mutual contract termination, which materialised on 13 June 2019 between
ATK and Lyngdoh.
East Bengal Lyngdoh was signed by
East Bengal Club for the
2020–21 Indian Super League. He played two games for the club before retiring to pursue a career in politics. ==International career==