The 68-year-old singer thought chatted about gay rights with Putin and posted an Instagram photo thanking the Russian President for the call, reported CNN.
Komsomolskaya Pravda, a Russian celebrity prankster known as "Vovan" - whose real name is Vladimir Krasnov - along with his partner, made the prank call to the British singer, playing the roles of Putin and a press secretary, after John said he wanted to meet the former to discuss gay rights in Russia.
"We thought Putin wouldn't want to meet him or call him at least in the nearest future, but it turned out Elton John's been waiting for such a call.
John thanked the Russian President in his Instagram post that led to a denial from Kremlin.
"Thank-you to President Vladimir Putin for reaching out and speaking via telephone with me today. I look forward to meeting with you face-to-face to discuss LGBT equality in Russia," John wrote, alongside a a photo of the Russian leader.
Krasnov has a history of making prank calls to celebrities and politicians, including former Georgian President Mikheil Saakashvili and Belarusian President Alexander Lukashenko.