They were first equal among the 30 busiest airports with 100 per cent scores, but Aberdeen was in joint second bottom place with 63 per cent.
Prestwick Airport in South Ayrshire was given a 75 per cent rating.
Netflights said Edinburgh and Glasgow's rating reflected the "significant investments they have both made in improving the airport experience for passengers with a range of disabilities in terms of service and facilities."
It said both "scored consistently well across its assessment criteria, which factored in elements like hidden disability lanyard schemes, initiatives to support hard of hearing and visually impaired passengers, and investments in Changing Places facilities".
The airports trumped next-placed Heathrow, with 96 per cent.
Worst rated was Doncaster Sheffield with 63 per cent.
The accolade for Edinburgh and Glasgow follows both airports receiving a "very good" rating from the Civil Aviation Authority in its airport accessibility report 2018-19.
The CAA said they were “the only airports with more than nine million passengers a year to achieve a very good rating”.
That marked a significant turnaround for Edinburgh, which was judged by the CAA three years ago as the worst in the UK - the only one of 30 airports to be given a "poor" rating.
Aberdeen airport said it had also been given a top-rated "very good" rating by the CAA this year.
Netflights managing director Andrew Shelton said: “For many years, airports have factored in the need to be accessible to everyone into their designs and renovations.
"While some are doing really well, as our review shows, several still have work to do to ensure customers with particular needs aren’t disadvantaged and can enjoy their airport experience as much as everyone else.”
Airports have 'worked very hard'
The Scottish Government-appointed Mobility and Access Committee for Scotland (Macs) advisors said Edinburgh and Glasgow's top rating was well deserved.
Aviation lead Hilary Stubbs said: "We are extremely pleased to see Edinburgh and Glasgow airports have been voted top in the survey.
"They have worked very hard to assist travellers with visible and hidden disabilities.
"We have worked closely with all Scottish airports and are very proud that seven of our eight largest airports are in the CAA ‘very good’ category.
"This achievement by the airports reflects on the work that Macs and Transport Scotland are doing to make transport accessible for everyone."
A spokesperson for Aberdeen Airport said: “Earlier this year we received the highest rating in the CAA’s accessibility report.
"To achieve a 'very good' classification, we had to demonstrate we provide high-quality support to passengers who require additional assistance as well as keeping in regular contact and consultation with our users.
"Within the report, the CAA praised us for our work with local disability groups through our forum, Access ABZ.
"We’re immensely proud our airport has been recognised as an inclusive environment for all and we will continue to come up with new ways of supporting and assisting our passengers.”