The average fee for a fixed-rate mortgage is now more than £1,000 - the most expensive for four years, according to Moneyfacts.
The financial information service said that borrowers and lenders tended to focus on mortgage interest rates.
Rates are now among the lowest ever seen in the UK mortgage market.
However, Moneyfacts said that some borrowers would be better off by choosing a slightly higher rate with a lower fee, or no fee, when they remortgaged.
"Those savvy borrowers heeding the advice to remortgage could find that moving deals can be a costly affair, especially if their preference is for shorter-term fixed rates. Therefore, with fees on the rise, it is more important than ever for borrowers to consider the true cost of a mortgage before obtaining a deal," said Charlotte Nelson, of Moneyfacts.
"Deals with larger fees often allow you to add the fee to the mortgage advance, however, this increases the amount borrowed, pushing up monthly repayments.
"The extra saved by opting for a deal with no fee could be better used to overpay the mortgage, which could help borrowers become mortgage-free quicker."
Figures from HM Revenue and Customs (HMRC) show that, on a seasonally-adjusted basis, property transactions have generally been close to the 100,000 mark each month for the past three years.
This climate, in part, has resulted in lenders launching new products to try to attract new borrowers, often with very low rates.
Moneyfacts said that, for those with a £150,000 mortgage and repaying over 25 years, some deals with the lowest rates on the market have fees of around £2,000, with one as high as £4,000.
The average fee for these customers was now £1,018, compared with £986 a year ago, and £886 in July 2014.
Homeowners are making a "costly mistake" by turning a blind eye to additional fees when they remortgage, it has been claimed.