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It's been stop and go for car- and ride-sharing companies such as Lyft, uberX, FlightCar and RelayRides at San Francisco International, but a new agreement has given one business a green light to operate legally at the airport.

That's good news for fans of RelayRides, a San-Francisco-based peer-to-peer car-sharing company that since August has provided departing passengers free airport parking and car washes, while offering arriving visitors great rental deals on those cars.

RelayRides, which has car shares available in 1,900 U.S. cities, had argued that it was exempt from having to pay the airport the same fees that traditional rental-car agencies pay because it operates in the shared-economy marketplace.

But that didn't sit right with SFO, which derives about 10 percent of its annual operating budget ($94 million in fiscal year 2011-12) from such fees.

( Read more: Beer in baggage claim tops off airport revenues)

The airport maintained that RelayRides and FlightCar, another business with an almost identical car-sharing service, must pay rental-car concession fees to operate at the airport.

San Francisco International has filed a legal complaint against FlightCar, but under the first such agreement between a sharing-economy company and a major U.S. airport, RelayRides has agreed to be classified as an off-airport rental.

That means that, just like any other off-site car rental company, it will abide by state and airport permitting, licensing and congestion-reduction rules. It also will pay SFO 10 percent of gross revenues from its airport-related transactions, plus a $20 per-transaction fee, said airport spokesman Doug Yakel.

A traveler heading to the airport can reserve a free parking spot for a qualified car at the RelayRides lot, and then take a shuttle to the terminal. RelayRides will wash the car and make it available to qualified renters at a rate the company touts as 20 percent to 40 percent less than traditional car rentals. It also provides owners with a $1 million liability policy.