Dr Kevin Moore, who was appointed to help turn the landmark into a major visitor attraction, left on October 31.
Details of the settlement agreement between the Bridge Board and Mr Moore, who is understood to have earned £126,000-a-year, have not been disclosed.
The last board meeting Dr Moore attended, according to the minutes, was in December 2018.
Caroline Lacey, the East Riding Council's chief executive was appointed acting clerk in April "in the absence of the clerk and chief executive", the minutes state.
Ms Lacey will continue in the role, pending a review of the management structure.
It comes after The Yorkshire Post revealed that a masterplan aimed at attracting an extra 400,000 visitors a year, which included the UK's first musical road, had been shelved.
Instead an unnamed operator has been lined up to develop a multi-million pound leisure facility at the bridge.
Dr Moore, formerly director of the National Football Museum in Manchester, is described on his Linkedin profile as a "globally acclaimed academic expert on museums, attractions, cultural, football and sports history".
He was appointed nearly three years ago but rarely gave interviews.
Chairman of the board Councillor Sean Chaytor said the board recognised the good work Dr Moore had done and wished him the best for the future.
Coun Chaytor said: "We would like to thank Kevin for all he's done. He did a first-rate job of reorganising things at the bridge.
"We now want to look at how the bridge is managed for the future."
The Grade One-listed Humber Bridge is still the longest single span suspension bridge that people can walk and cycle over.