Martha Rafferty, 42, said a handful of items would be up for grabs including classic guitars, awards and discs, along with the scribbled lyrics to both Baker Street and Shoeshine Boy.
The Paisley-born singer became a household name when the song was released over 25 years ago.
Now the words which launched his career have been handed over to Bonham's auctioneers for sale this December.
Making the announcement on Facebook, Ms Rafferty said: "Just sent a bunch of things down to London for auction. All up for grabs in December. Time to clear a space so new things can happen."
The news provoked a strong response from fans, while family and friends urged Martha to reconsider.
Gerry's cousin, Alan Rafferty, told Martha: "I think you would end up hugely regretting parting with them. A sheet of A4 doesn't take up much space."
Several others also responded by urging Martha to donate the items.
Fan Mick McCarthy said: "It would be extremely foolish to sell the handwritten lyrics to Baker Street.
"They're priceless, both financially and historically, he added. "Lend them to a museum perhaps, but keep them for your family."
Colin Nimmo said: "This deserves better than to be on some millionaire's wall."
"Please don't sell the lyrics," Stevie Stone begged. "So much heart and soul went into those by the master. I could never let them go, even if i was penniless."
However, Ms Rafferty admitted: "I like the idea of a Paisley museum though. Will look into that."