The 36 year old originally from Luttrell Park in Carpenterstown, Dublin, had travelled to Cork where he became involved in a row with another person on Patrick's Quay.
Gardai believe that Mr Flanagan, who had been living in hostel accommodation in the capital, was assaulted sometime around 10pm on Thursday at the Patrick's Bridge end of the quay.
He was found collapsed and rushed to Cork University Hospital where he underwent emergency surgery for a brain injury.
However he failed to regain consciousness and was pronounced dead early Saturday morning.
Gardaí are refusing to release the findings of a post-mortem but confirm they are treating his death as suspicious.
Witnesses are being asked to contact Mayfield Garda Station.