The country's SANA news agency reported on Sunday that the amnesty includes those who participated in peaceful anti-government demonstrations.
It also includes those who have possessed unlicensed weapons and ammunition and those who would hand over their unlicensed weapons to the government before the end of January.
The report did not say how many prisoners would be affected by Sunday's presidential decree.
The decree came after Qatari Emir Sheikh Hamad bin Khalifa Al Thani called for a military intervention in Syria.
Syria has been experiencing unrest since mid-March and the UN said more than 5,000 people have been killed in the country over the past nine months.
Damascus says over 2,000 of those killed were members of its security forces.
The West and the Syrian opposition accuse the government of killing protesters. Damascus blames ''outlaws, saboteurs and armed terrorist groups'' for the unrest, insisting that it is being orchestrated from abroad.
The head of the Arab League mission, Sudanese General Mohammed al-Dabi, will report about the situation in Syria on Thursday and Arab foreign ministers will then decide whether to continue the mission, or possibly refer Syria to the UN Security Council.