When Sonoma-Marin Area Rail Transit system trains begin rolling later this year it will take 67 minutes to go from the Sonoma County Airport to downtown San Rafael during weekdays, according to estimates by the agency, which is starting to develop a schedule.

Peak service has been sketched at between 5 a.m. and 10 a.m. and from 3 p.m. to as late as 9 p.m. for the last trains pulling into Santa Rosa, according to SMART. There will also be one midday train for people going to work late or who have to leave early, rail officials said last week as they looked over a draft schedule. There would be a train every 30 minutes during commute times.

Weekend and holiday service has also been looked at and would be designed to link up to Larkspur ferries. But in Marin that would involve taking a bus or shuttle from downtown San Rafael to the ferry terminal. Rail service to Larkspur, however, could be in operation by 2018.

“Weekend service might be more viable when (trains) get to Larkspur,” said Tom Madoff, SMART’s operations director.

SMART officials are promising rail service will deliver people to destinations faster than taking Highway 101, in particular those coming southbound on the freeway in the morning.

“The alternative and options trains will be providing is tremendous,” said Farhad Mansourian, SMART’s general manager.

SMART’s draft schedule shows a morning a trip from Railroad Square in Santa Rosa to the Marin Civic Center taking 49 minutes. By car that trip is 90 minutes, according to SMART.

And a typical Highway 101 commute from Petaluma to the Civic Center that would take 40 to 75 minutes would be 25 minutes by train. The 45-minute Highway 101 commute from San Marin in Novato to the Civic Center would be reduced to 14 minutes, rail officials said.

“That’s a key benefit to having our own dedicated track (that is) not subject to traffic or congestion,” said Jeanne Mariani-Belding, SMART spokeswoman.

The times developed by SMART are based on computer simulations and will be put to real life testing in June. They can then be adjusted if needed, said rail officials, who have not announced a specific time frame for the start of service.

When trains begin rolling, passengers will pay to go from zone to zone instead of one flat fare. Under the plan there would be five zones overall and two zones in Marin, with the border between San Rafael and Novato the demarcation point. The cost of fares has not been announced.

What is known is that only Clipper will be accepted for fare payment. Clipper will make it easier for SMART riders to transfer to other transportation systems, such as Golden Gate Transit, officials said.

As envisioned, SMART train station platforms would have Clipper vending machines and card readers for passengers. Scanners will be used by SMART employees on trains to make random fare checks to catch any scofflaws who board without using Clipper cards. There will be retail locations in the community where riders can pick up and load Clipper cards.

The Clipper card system is similar to FasTrak, which allows drivers to pass through Bay Area toll booths without having to stop and hand over cash. Clipper works much in the same manner, with patrons signing up and allowing their credit cards to have bus, ferry or rail fares deducted.

Clipper users can scan or “tag” their cards on a reader. A computer chip inside the card reads the transaction, information is displayed on the screen and a beep sounds to alert the passenger the card has been read. The Clipper system automatically deducts the correct fare and applies any discounts — including transfers — for each trip.