It is the latest move by Amman to normalise ties with the Bashar Al Assad regime.
The announcement came on the second, and last, day of a visit by a Syrian ministerial delegation to Jordan to agree on easing border restrictions.
Royal Jordanian, which is majority-owned by the government, suspended flights to Syria in 2012, citing security reasons.
Meetings between the two sides increased after Jordan’s King Abdullah visited Moscow five weeks ago and met President Vladimir Putin.
The pair discussed the “normalisation of the situation in Syria”.
Moscow has been encouraging regional governments to restore full ties with the Syrian regime and help pay for reconstruction, Western diplomats in Amman say.
Moscow's intervention in 2015 sharply tipped the military balance in the regime’s favour, helping it to reclaim large amounts of territory.
An official statement said Royal Jordanian will “return to operate passenger flights between Jordan and Syria” as of October 3.
The airline used to fly to both Damascus and Aleppo.
After the meetings between trade, water, electricity, agriculture ministers this week, the two sides agreed to revive talks on a dormant free-trade zone on the border.
They also agreed on a “road map to reactivate the line linking the Jordanian-Syrian electricity network,” the statement read.
Jordanian officials said on Monday that restrictions were also eased on the main passenger and lorry crossing with Syria at Jaber-Nasib.
Cargo will no longer have to be offloaded on to Syrian lorries when crossing the border and vice versa.
Although the Jaber crossing has been open since 2018, after the Syrian government drove rebel groups from southern Syria, trade has yet to recover to the $1 billion prewar level.
“We hope the moves will restore previous trade dealings before the conflict and revive lucrative transit trade,” Jamal Al Rifae, deputy head of Jordan's chamber of commerce, told Reuters.
Unlike Gulf countries, Jordan did not sever diplomatic ties with Syrian in response to its crackdown on the initially peaceful 2011 revolt against five decades of Assad family rule.
Sunnis, particularly in rural areas on the border with Jordan and elsewhere in Syria, formed the backbone of the revolt.
Majority Sunni Syria has been ruled by members of its minority Alawite community since mostly Alawite officers took power in a 1963 coup.
Jordan, a staunch US ally, hosted rebel commanders and members of the opposition to Bashar Al Assad.
It has been shifting towards accommodation with the regime since the Russian intervention in 2015.
Amman regards its policy of boosting ties with the Syrian regime as pragmatic, the Western diplomats say.
But, the kingdom has been worried by increased drug smuggling from regime areas, and pro-Iranian militias that have consolidated their presence in the past year in Syrian territory near Jordan, they say.
Drug smuggling and terrorism were the focus of a meeting in Amman this month between the Jordanian and Syrian chiefs of staff in Amman, official Jordanian media said.
One of the diplomats said that Russia played a major role in arranging the meeting.
He said that the cash lure from the drugs and Iran's role in south Syria will make it difficult for Jordan to realise its strategic goals from boosting ties with Mr Al Assad.
"Russia's influence on Assad and his allies is ultimately balanced by Iran," the diplomat said.