LionsXII were set a target of finishing top five for the 2013 Malaysia Super League. Five senior players, namely Shahril Ishak, Isa Halim, Fazrul Nawaz, Irwan Shah and Baihakki Khaizan were included in the 29-men squad to guide the younger players. Other key players such as Shahdan Sulaiman and Shaiful Esah no longer featured. The main aim was to develop the U–23 players and prepare them for the upcoming 2013 Southeast Asian Games that would be held at the end of the year.

LionsXII began their campaign by defeating ATM FA 1–0 away. Subsequently, they vanquished the nation's traditional rivals Selangor FA. However, LionsXII stumbled to three losses against lowly T-Team FC and PKNS FC away. One sent them crashing out of the 2013 Malaysia FA Cup. In a turn of events, LionsXII went on a long unbeaten streak, securing important wins over Pahang FA (3–0), Kelantan FA (1–0), and ATM FA (3–1) at home.

On 2 July 2013, a 4–0 win over relegation-threatened FELDA United FC in the penultimate league game made LionsXII league champions. Singapore's Prime Minister, Lee Hsien Loong was present for the match played in front of a sold-out crowd at the Jalan Besar Stadium. The MSL trophy was also brought to the stadium as the LionsXII received it on home soil after the final whistle. LionsXII became the first foreign team to win the MSL, adding to the four Malaysian league titles it had won in 1979, 1981, 1985, and 1994. The title run was defined by a combination of good defence (15 goals conceded, the best record in the MSL) and goals from set-pieces (17 out of 32). The club chalked up their best home record (10 wins and 1 draw) in the league, making Jalan Besar Stadium a fortress.

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