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.

Jack Galsworthy, from Cornwall, and Freddie Wright, from Gloucestershire, both 21, are one week into their 3,000 mile challenge and their "morale is high" after initial seasickness.
The pair are aiming to raise Â£150,000 for the Brain Research Trust.
They caught and ate tuna which they had as sushi for Christmas dinner, their team said.
They will be rowing two hours on and two hours off for three months in the race from La Gomera to Antigua, as part of the Talisker Whiskey Atlantic Challenge.
Two days from the nearest support team, they risk facing 40ft waves, sharks, howling winds, blisters, salt-rashes, sunstroke and sleep deprivation.
The Atlantic Castaways team spokeswoman Alexandra Durnford, said they were suffering badly from sea sickness at first but have now recovered and "morale is high".
"They tried their luck at a bit of fishing and managed to catch a very small tuna and had sushi I would imagine as there are no cooking supplies on board, so they did have a very special Christmas lunch, just an unusual one," she said.
The duo are expected to lose at least 15% of their body weight during the challenge, which they hope to complete in 90 days time.

It started happening when Apple's operating system, iOS 8.3 came out.
By tapping and holding on a chosen emoji, iPhone users of iOS 8.3 or above are now given the choice between five different skin tones and new flags.
Apple users who are still using iOS 8.2 and below are not able to see the new emojis.
Instead they are replaced with a picture of an alien face inside a black square, next to the original emoji.
Apple wouldn't give us a comment on this, but on their website it says: "If you get a message with unexpected characters instead of emoji, try updating your iPhone, iPad, iPod touch or Mac."
If you're viewing the new iOS emojis on devices other than Apple they can appear as lots of other things, like blank spaces, boxes, equal signs, question marks, or even line breaks.
Homeowners are making a "costly mistake" by turning a blind eye to additional fees when they remortgage, it has been claimed.
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Two university students have begun their bid to become the youngest pair ever to row across the Atlantic Ocean.
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Have you noticed any of these little guys creeping into your texts and social media, when you know they weren't intended to be there.