The deal that will see the EU issue 750 billion euros of joint debt to help member states hit by the coronavirus pandemic marks a historic step towards a deeper fiscal integration in Europe.
EU leaders also approved the bloc's 2021-2027 budget worth over 1.8 trillion euros.
Diplomats say the overall EU support for Lithuania in the next financial framework will be 1.7 billion euros higher than in the 2014-2020 budget period.
The Baltic states secured a better deal on agriculture subsidies at the end of the marathon summit. Direct payments to Lithuanian farmers will increase to 200 euros per hectare in 2022, from the current 117 euros.
Lithuanian President Gitanas Nauseda hailed the deal on bigger subsidies as the Baltic countries' most important achievement that will help ensure a more level playing field in Europe.
"We have a great offer for farmers," the president said in a comment to the media.
"Direct payments can be seen in one way or another, but they are part of the common agricultural policy and I, as an economist, attach great importance to equal competition conditions," he said.
Cohesion support, the other key line for Lithuania, did not change in the final stage of the talks.
Cohesion funding for Lithuania may be slashed by up to 24 percent in the 2021-2027 budget compared with the current period, because the country's economic indicators have moved closer to the bloc's average.
The cut may be somewhat offset by compensation for losses caused by emigration. For Lithuania, it would amount to around 180 million euros.
The new budget earmarks 490 million euros for the decommissioning of the Ignalina nuclear power plant.
Funding for the Kaliningrad transit scheme that allows Russian citizens to cross Lithuania's territory under a facilitated procedure was increased by 50 million euros to 189 million euros during the summit.
Lithuania will be eligible for around 2.4 billion euros in grants and another 2.2 billion euros in loans from the new economic recovery fund, according to the president's office.