The product, which launched in June, was the lowest rate ever to be offered, according to data firm Moneyfacts.
It was offered at up to 65% loan-to-value (LTV) and came with a £1,499 fee.
The bank put the move down to the rising cost of funding.
In a statement, HSBC said: “When the cost of funding comes down we are always quick to pass on the benefit to customers, and we have been able to do that for almost six months with our 0.99% rate mortgage. The cost of funding has gone up over the last month or so and we have had to reflect that in our recent pricing review.
“We regularly review our rates, and while they still provide good value for those looking to move onto or up the housing ladder, should the cost of funding come back down you can be sure we will reflect that with some great deals.”
Over the past year borrowers have been treated to some of the lowest mortgage rates on record, but Charlotte Nelson of Moneyfacts said, “time is perhaps up on the lowest deals in the market”.
“We all knew these deals wouldn’t last forever, but with market uncertainty and rising swap rates it is increasingly difficult for providers to offer some of the lower deals in the market,” she said.
“Borrowers might feel as though they blinked and missed the lowest rates on the market, for this reason, borrowers need to galvanize themselves now if they want to make the best of the low rates that are still around.
“Fixed mortgage rates are still very low in comparison with a year ago, so borrowers who are sitting on their SVR or coming to the end of their mortgage deal need to decide whether they are willing to miss the opportunity to fix to a low rate.”
