The fear of conscription, and potential punishment for ducking it or for desertion, is frequently cited by aid groups as one of the main reasons refugees give for not wanting to return home.
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’s foreign-backed insurgency that began in 2011 has led to half a million deaths.
Many soldiers deserted, some to join the militants and others to escape the fighting. More than half the pre-war population fled their homes. About 5 million went abroad and millions of others were displaced within Syria.
While the amnesty covers desertion, it does not cover fighting against the government or joining the terrorists.