Activists said a device exploded next to a car in which Col Riad al-Asaad, long head of the Free Syrian Army (FSA), was travelling in Mayadeen.
There were conflicting reports about his fate, but an FSA spokesman told BBC Arabic that he had lost a leg.
Col Asaad once led the armed rebellion against President Bashar al-Assad, but his position was gradually superseded.
In December, more than 260 leaders of the main FSA units from across Syria agreed at a meeting in Antalya to a unified command structure.
They elected a 30-member Supreme Military Council (SMC), which then chose Gen Salim Idriss as the new chief of staff.
Col Asaad said he had not been invited to the meeting by the foreign powers which organised it, adding: “They want people who obey orders.”
The former Syrian Air Force commander, who defected in July 2011, nevertheless remained a prominent figure in the armed uprising, regularly appearing with rebel fighters on the ground in Syria.
The Syrian Observatory for Human Rights, a UK-based activist group, reported that Col Asaad had been conducting a tour of the eastern town of Mayadeen on Sunday night when a bomb exploded near his car, wounding him in the leg.
An FSA spokesman confirmed to BBC Arabic that Col Asaad had lost the leg.
A relative told the AFP news agency that he had been transferred to a hospital in Turkey for treatment. His condition is reportedly stable.