The carriers have agreed to include debit card surcharges in the headline ticket price rather than at the end of the booking process, the Office of Fair Trading (OFT) said.
The airlines also agreed to make surcharges for credit cards more transparent so these fees will be clearer and easier to find during the booking process.
Aer Lingus, BMI Baby, Eastern Airways, easyJet, Flybe, German Wings, Jet2, Lufthansa, Ryanair, Thomas Cook, Thomson (TUI) and Wizz Air were subject to an OFT consumer law investigation and have agreed to change their practices.
Clive Maxwell, the OFT's chief executive, said: "It is important that the cost presented when customers search for a flight is realistic and that they are not surprised by extra charges."
The Government has also announced plans to bring forward legislation to ban excessive debit and credit card surcharges, which cost consumers £300 million a year from the airline sector.
The OFT said people should not have to incur surcharges to use a debit card online as they are the "online equivalent of cash" which means that headline prices should be the price people can pay.
However, the OFT said traders may still impose surcharges for credit cards, which can be more costly to process.
Eastern Airways, easyJet, Flybe, German Wings, Lufthansa, Thomas Cook, TUI and Wizz Air have already made changes to their pricing structures, websites and marketing materials. Other airlines will change their advertising practices by August 1 and fully complete further changes over the coming months.
Mr Maxwell added: "We made it clear from the start that we would use all of our enforcement powers, including court action if necessary, but are pleased to have reached agreement with the airlines before court proceedings were required."
The watchdog launched a 90-day investigation in March after a super-complaint from independent consumer body Which? highlighted consumer anger about the increasingly widespread use of surcharges.
Which? chief executive Peter Vicary-Smith said: "Over 50,000 people supported our campaign to end rip-off surcharges, so it's good news that debit card surcharges will be displayed in the headline price of flights – as long as the airlines don't use this as an excuse to push up their prices."
He added: "The OFT should make sure that all companies are taking these steps, not just airlines.
"We're pleased that the Government has said they are sticking to their original time-table to ban excessive card surcharges by the end of the year."