The Grade II* listed landmark was built in 1871 and was the city’s former Dock Offices.
It underwent the renovation as part of the Hull Maritime Project, which was funded by Hull City Council and the National Lottery Heritage Fund.
Insider Media said the refurbishment had overcome a number of issues including “deterioration within the roof structure and asbestos, including aerosol contamination within a lift shaft”.
The judging panel praised the “attention to detail” in the renovated building as “exceptional”.
“The building’s use now has a much wider purpose than it once did and is all part of a wider programme of civic regeneration,” they added.
Ross said: “The success of the museum reflects the dedication, skill and passion of everyone involved in the project and demonstrates the value of investing in our heritage assets.
“We are incredibly proud that Hull Maritime Museum is being recognised as the very best refurbishment and restoration projects in Yorkshire.
“The thousands of visitors since it reopened have recognised the quality of the museum, so it is pleasing to see it now get the recognition of this award.”
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