According to the application before the zoning board, the new mixed-use, six story building (including a cellar), would include 769 square feet of retail space, 14 residential units, and two parking spaces.
The building was to be built on First and Washington Streets on the Walgreens parking lot.
The application requested several zoning variances and preliminary site plan approval.
According to the plan's architect, John Nastasi of Nastais Architects, they needed a variance from the zoning board for 80 percent lot coverage.
He said the request was reasonable as the buildings next door have 100 percent and 90 percent lot coverages.
First Ward Councilman Michael DeFusco said he believes many residents in his ward will be disappointed to hear Shake Shack won't be coming to town.
Nastasi said he was not sure if they will pursue recourse through the Hoboken Planning Board.