Highlights of the sale will include a guitar the musician played at the Cream reunion shows in 2005, estimated to sell for more than Â£13,000.
More than 150 lots will be auctioned in the New York sale next year.
Money raised will go towards the Crossroads Centre in Antigua, which Clapton founded in 1998 to help treat drug and alcohol addiction.
The sale will also feature a vast collection of amps and speakers, including a pair of Marshall speaker cabinets.
Used during the 1970s when the star was performing with Derek And The Dominos, it is expected to fetch more than Â£5,000.
Guitars donated by Jeff Beck, JJ Cale and Joe Bonamassa will also go under the hammer.
“We are delighted to be offering such a fantastic collection of guitars and amps from such an iconic musician,” said Stephanie Connell, head of entertainment memorabilia at Bonhams
She said she hoped the auction would “raise a lot of money for this worthwhile cause.”
Clapton has previously held auctions in 1999 and 2004.
In the latter, Clapton’s treasured Fender Stratocaster – called “Blackie” – fetched a record $959,500 (Â£607,500) at auction.
Items will go on display at Bonhams in London from 23 to 26 January before the sale on 9 February.