Anton Sorokow, who performs with the Vienna Symphony Orchestra, missed his flight after staff insisted the fiddle had to go in the hold as the cabin was full.
But the freezing, high-altitude temperatures in the hold could damage the violin beyond repair.
As a result, he had to cancel a lucrative job in Italy.
His 276-year-old Guarneri “del Gesu” violin is on loan from the Austrian National Bank and is insured for €4million.
EasyJet has apologised, but the Austro-Russian musician says he will avoid using the airline again.
Mr Sorokow, 40, a professor at the University of Music and Performing Arts in Vienna, said: “This has never happened to me before, in all my years of flying as a professional musician. I will certainly avoid flying with them again.
“I arrived 25 minutes before the plane was due to depart – but they told me the cabin was full. I tried to explain to them that it was a very expensive instrument; that if I put it with the rest of the baggage it would be badly damaged. It would have [invalidated] my insurance policy to do this. But they didn’t understand anything.”
The incident happened as Mr Sorokow tried to board a flight from Milan to Bari in southern Italy on October 30.
In a post on the music website Slipped Disc, he wrote: “It is a completely disastrous situation, which unfortunately, nowadays, can happen to every violinist???
“The consequences: 30 students at the Conservatorio de Bari were deprived of an important masterclass because one half-trained clerk at easyJet could not read the rules.”
The maker of the violin, Cremonese Giuseppe Guarneri – nicknamed “del Gesu” – is regarded as one of the great masters of violin making.
His instruments have sold for up to £10million.
Mr Sorokow said the experience had caused him “huge damage personally and professionally”, as he was due to be paid several thousand euros for the masterclass.
EasyJet has now apologised and has reimbursed Mr Sorokow for his ticket.
However, he said his lawyers are in talks with the airline regarding further compensation.
He added that “we must find a solution” to what has become a recurring problem for musicians.
In January this year a student started a crowdfunding campaign when her cello was smashed after being placed in the hold on a domestic US flight.