Laura Kuenssberg challenged the chief eurocrat as he posed for photos alongside the prime ministers of Poland, Latvia, Estonia and the president of Lithuania in Brussels.
Mr Juncker came under fire from MEPs after he urged Mr Putin to strike up a close security relationship with the EU while completely ignoring Theresa May’s allegations of Kremlin involvement as Russian double agent Sergei Skripal and his daughter Yulia in Salisbury.
As the Commission President moved away from the press pack, Kuenssberg shouted out a question about his letter congratulating Mr Putin.
Mr Juncker, looking rather sheepish, replied: “I wrote the same letter as Mrs Merkel – ask Mrs Merkel if it was the right thing to do.”
After the altercation, the BBC’s political editor tweeted: “Juncker didn’t look very happy when we asked him about congratulating Putin.”
German Chancellor Angela Merkel also sent the Russian President a letter after he was re-elected for another six years.
Leading Conservative MEP Ashley Fox joined the fury against Mr Juncker, branding his letter “nauseating”.
Mr Fox said: “To congratulate Vladimir Putin on his election victory without referring to the clear ballot rigging that took place is bad enough.
“But his failure to mention Russia’s responsibility for a military nerve agent attack on innocent people in my constituency is nauseating.
“The European Commission President is appeasing a man who poses a clear threat to Western Security.”
Nigel Farage mocked so-called “European solidarity” as he spoke to Express.co.uk about the both Mrs Merkel and Mr Juncker praising Mr Putin.
Mr Farage said: “So much for European solidarity, Ms Merkel did the same on Sunday!
“Listen, when it comes to British interests, they’re not really interested.”
And Tory MP Sarah Wollaston called Juncker’s letter “shameful”.
The Putin congratulations even drew anger from Euro-allies Donald Tusk and Guy Verhofstadt.
The latter said: “This is no time for congratulations.”