The consumer championing site found GoCompare was the “worst” and Skyscanner the “best” over a range of categories, including user-friendliness, price and market coverage.
It asked 2,200 people about their experiences over the past two years using the websites.
GoCompare received a score of 45% and Skyscanner, which was rated best for flight comparison, was awarded 69%.
Skyscanner was the only website to score four stars on value for money.
Tripadvisor came second overall and top for hotel comparison, receiving three stars across all categories in the survey.
However, earlier this year Which? Travel warned holidaymakers after it found suspicious reviews were artificially raising scores on Tripadvisor.
“Holidaymakers are known to spend hours and sometimes days looking for the best hotel rates and the best airfares, so for many of us, travel comparison sites are the first port of call,” said Rory Boland, Which? Travel editor.
“There are really only one or two sites you should consider using if you want to save yourself both money and time.”
In a separate investigation, Which? Travel pitted comparison sites against each other to see which consistently found the best price.
Skyscanner produced the cheapest price six out of 10 times. Google Flights found the cheapest fare once and the most expensive fare three times.
For hotels, Kayak sourced the cheapest deal six out of 10 times. It was closely followed by TravelSupermaket, which found the cheapest price 40% of the time and also the expensive rates 40% of the time.
A spokesperson for GoCompare said: “We are disappointed by the results of Which?’s research and will be looking over the results to understand where we can improve these services to give people the best experience possible when using GoCompare.
“As pointed out by Which?, while we specialise in areas such as car and home insurance, we use third party providers for other services which appeal to our customers.
“While Skyscanner, who provide our flights comparison, came top in Which?’s research, we take our responsibilities as an introducer to third-party providers very seriously and will make sure the functionality on our site reflects this.”
