Faced with a multimillion-dollar budget shortfall and flat ridership, BART is taking the first step toward a possible fare hike.

“Nobody wants to increase fares or reduce service or do anything that has an impact on riders,” said Rebecca Saltzman, president of the BART Board of Directors. “But we have to consider all options.”

Among the possibilities:

•Increasing the minimum fare.

•Charging people more if they use paper tickets instead of Clipper cards.

•Reducing discounts for youths, seniors and disabled people.

When it meets Thursday, the BART board will consider authorizing a fare-increase study, which the federal government requires before a transit agency can raise prices. The study will look at the effects of fare hikes on minority and low-income communities.

BART fares are already set go up across the board in January by 2.7 percent under a policy the agency has adopted to raise prices automatically to track inflation. That will raise the cost of a $5 ticket by 10 to 15 cents.

The fare changes that BART is considering now would be more select.

The minimum fare of $1.95, which is scheduled to increase to $2 under the automatic fare-adjustment policy, could rise to $2.25 under the proposed new plan. BART officials say the change would bring rates for a single ride closer to those charged by other transit agencies. Muni charges $2.50, AC Transit, $2.10 and SamTrans, $2.25.

In an effort to persuade riders to use Clipper cards, BART is also contemplating charging more for paper tickets with magnetic strips, most of which are bought at station machines. About one-third of BART riders use the paper tickets.

The fare-increase study will look at charging 10 percent, 25 percent or a flat 50 cents per ride extra for using paper tickets. A 25 percent fare increase would boost the cost of a ride from Dublin/Pleasanton to San Francisco International Airport from $11.60 to $14.50.

BART says fares paid with Clipper cards cost less for the agency to administer and process. Clipper users tend to have larger balances on their cards and reload them less frequently, which reduces lines at ticket machines, particularly after sporting events and concerts.

BART officials emphasized that they are not considering eliminating magnetic-strip tickets, as the Washington Metro system did about a year ago. But BART is making it harder to buy the tickets away from stations — several months ago, it cut off sales at several places in the Bay Area where they had been available, including a pair of senior centers in Oakland.

In addition to fare hikes, BART is also looking at reducing the discount it offers to seniors, children under 13 and people with disabilities, from the current 62.5 percent markdown to 50 percent. Most other Bay Area transit agencies offer discounts at or near 50 percent. However, BART will also consider extending the youth discount to 18 years old, consistent with most regional transit systems.

Not surprisingly, an unscientific survey at BART’s Powell Street Station in San Francisco turned up no fans of a fare increase — especially the possible 25 percent markup for using the type of ticket that has been sold at stations since trains first started running in 1972.

“Everything goes up, but 25 percent is huge,” said Javier Bello of San Francisco.

BART patron Hugo Montoya of Emeryville said he would tolerate a slight fare increase if the system would run its trains all night, like the subway in his native New York.

“But not 25 percent,” he said. “Before they raise the fare, they should do something about the service.”

BART says it needs to stop running trains in the early-morning hours so it can do track maintenance.

Adopting all the proposed fare changes could raise as much as $20 million, BART officials say. They would be enacted at a time when the system is facing a projected budget deficit of $25 million to $35 million for the budget year that starts July 1 and ridership that is stagnating.

After years of increases, the number of people taking BART has flattened out, said agency spokeswoman Alicia Trost. BART is puzzling over a 9 percent decline in weekend passenger totals.

In addition to considering fare hikes, BART is leaving some open jobs unfilled and has cut consultant contracts. Directors are also considering higher parking charges, more advertising, and service cuts, including starting trains an hour later in the morning.

Michael Cabanatuan and Steve Rubenstein are San Francisco Chronicle staff writers. Email: mcabanatuan@sfchronicle.com, srubenstein@sfchronicle.com. Twitter: @ctuan, @SteveRubeSF