The agreement, worth an estimated $2.2 billion, would include building a branch of a prospective major natural gas pipeline and a major gas storage facility in Serbia. It also envisages Russia's state gas monopoly, OAO Gazprom (GAZP.RS), acquiring a controlling stake in Serbia's state oil company NIS.
Belgrade has turned increasingly away from the West and toward Russia, which has supported Serbia in the debate over independence for the province.
Serbia's President, Boris Tadic, thanked Moscow for its support on Kosovo at the start of his talks with Putin.
"Serbia very deeply respects the position of Russia on Kosovo," Tadic said. "We will defend our interests in Kosovo, operating on the basis of international law and we will never do otherwise."
Moscow last year threatened a veto in the U.N. Security Council to block a Western-backed plan for internationally supervised statehood for Kosovo.
Russia has used the rift to strengthen business and diplomatic ties to Serbia - with which Moscow has historic cultural and linguistic ties.
Serbia endorsed the energy deal days after Putin won Bulgaria's support last week for the project, known as the South Stream pipeline, which would further strengthen Russia's dominance of the European Union energy market.
The 900-kilometer, EUR10 billion South Stream pipeline would run under the Black Sea from Russia to Bulgaria, where it could branch off in several directions. The project undercuts the prospective U.S.- and E.U.-backed Nabucco pipeline designed to ease Europe's reliance on Russia.
Tadic and Serbia's Prime Minister Vojislav Kostunica will both attend Friday's signing of an inter-government agreement on cooperation in the oil and gas industry, the Kremlin said.