In a decree issued on his social media feeds, Syrian President Bashar al-Assad said the amnesty covered all punishments for desertion inside or outside Syria, Reuters reported.
Men inside Syria will have four months to take advantage of the amnesty while those outside will have six months.
Under Syrian military law, deserters can face years of prison if they leave their posts and do not report for service within a set amount of time.
Syria has been gripped by civil war since March 2011 with various terrorist groups, including Daesh (also known as ISIS or ISIL), currently fighting against the central government.
Syrian troops defeated Daesh late last year and took back all the urban bastions once the terror group had under its control, but the group's remnants have been trying to regroup and have mounted a series of hit-and-run attacks.