[1] In the summer of 2008, he went on trial with KF Tirana, where he was spotted by the head coach Blaž Slišković, who was impressed with the 19-year-old and signed him ahead of the 2008–09 campaign.

The following season, Lilaj made his European debut in the Second qualifying round of the 2009–10 UEFA Champions League against Norwegian side Stabæk, a match which ended in a 1–1 draw.

[5] He came on at half time for Blerti Hajdari in the 2009 Albanian Supercup as they defeated 1–0 Flamurtari Vlorë, which beat them in the previous cup final.

[12] He was then allowed to leave the club at the end of the season, as did many other first team players, including Andi Lila, Jahmir Hyka, Tefik Osmani and Pero Pejić.

In the summer transfer window of 2011, Lilaj joined Croatian Prva HNL side NK Lokomotiva, where he struggled to compete with the likes of Mateo Poljak and Marcelo Brozović for a first team place.

Despite having a difficult personal season, his performances did attract the interest of Albania national team head coach Josip Kuže, who gave him his first senior international call up and cap.

After one season in Croatia, he left Lokomotiva to return to Albania, where he was subject to interest from a host of Albanian Superliga sides in the summer of 2012.

[14] There he found his old Tirana teammates, including Ditmar Bicaj, Ivan Gvozdenović, Pero Pejić, Sebino Plaku and Daniel Xhafa.

On 3 October 2012, Lilaj scored his first goal in nearly 20 months against Olimpik in a 7–2 Albanian Cup win which also saw him receive a red card in the 85th minute.

[24] They did, however, qualify for the play-off round of the Europa League, where they were drawn against Ukrainian side Chornomorets Odesa,[25] with the first leg in Ukraine ending in 1–0 loss for Skënderbeu.

[27] On 12 August 2014, Lilaj signed a two–year contract with Polish Ekstraklasa side Ruch Chorzów, where he even completed his medical and was presented to the media,[28][29] only for the move to be annulled.

[32] Later on 5 November 2015, Lilaj scored twice in just under 20 minutes as Skënderbeu recorded a 3–0 victory over Sporting CP in the 2015–16 UEFA Europa League group stage.

[33][34] His first goal was scored after teammates Peter Olayinka and Esquerdinha missed opportunities, but Lilaj netted in the rebound to put Skënderbeu ahead 1–0.

Lilaj scored the resulting penalty past substitute goalkeeper Marcelo Boeck to put Skënderbeu 2–0 up at the Elbasan Arena.

[38] His goal from a narrow position in the returning leg of second qualifying round against Kairat on 20 July was deciding as Skënderbeu won 2–0 and progressed 3–1 on aggregate.

[61][62] Lilaj was first approached to Albania senior team by manager Josip Kuže for the last UEFA Euro 2012 qualifying matches against France and Romania respectively on 7 and 11 October 2011.