The loss has been put down to huge restructuring of the organisation by Pope Francis as he attempts to stamp out corruption.
Profit went from 86.6m Euros in 2012 to just 2.9m Euros in 2013.
The Vatican spent 7.3m Euros bringing in American anti-money laundering experts to vet 18,000 individual Vatican Bank accounts.
Allegations that the Vatican Bank was used by money launders forced Pope Benedict to start a process of reform at the organisation.
He appointed Ernst von Freyberg just before his retirement in February last year.
He'll now be replaced by French businessman Jean Baptiste Franssu.
The president was appointed by Pope Benedict just before his retirement in February last year.
Financial figures also show The Holy See, the administrative headquarters of the Catholic Church, was 24.2m Euros in the red last year.
But the Vatican State made 32.3m Euros in profit in the same period, mainly from ticket sales for the Vatican Museums.