Samaraweera, along with five other Sri Lanka cricketers, were injured in the 3 March 2009 attack on the bus that carried the Sri Lanka cricketers to the Gaddafi Stadium. He was hospitalised with a thigh injury. Samaraweera was the most seriously injured player amongst them. Thilan suffered a major injury on his left thigh as a bullet fired by a terrorist pierced through his knee well inside his body by 12 inches. Six policemen that guarded the bus and two civilians were killed in the attack. He then underwent surgery, remained at hospital for two weeks and took brief break from cricket for roughly 4 months. The doctors advised him that he may not ever play cricket again but he soon overcame the obstacles and mental trauma following the attack. He also revealed that he was still haunted by the 2009 Lahore terrorist attack. He returned to cricket in June 2009 following his surgery. He was believed to have undergone 2 and half hours operation at the Nawaloka Hospital in Colombo and fears were also raised that he could be forced to retire from international cricket.