For nearly a century, putting your savings in a federally insured bank has been a safe bet: If the institution fails, up to $250,000 of your money will be protected.

What if it isn’t anymore?

The promise of bank insurance, a cornerstone of U.S. consumer protection since the Great Depression, is now being tested by a crisis centered around online lenders with hundreds of millions of dollars in deposits between them. Customer accounts have been frozen, preventing people from cashing out their life savings. Most depositors have little clue where their money went and whether they’ll get any of it back.

The crisis began this spring with the collapse of Synapse Technology, the kind of company you’ve probably never heard of unless you’ve suffered through all the fine print on your bank statements. It ran banking software for fast-growing online lenders with names like Juno, Yieldstreet, and Yotta.

Backed by some of Silicon Valley’s biggest venture capitalists, the startups offer accounts that charge lower fees and pay much higher interest rates than traditional banks. Their flashy websites advertise insurance from the Federal Deposit Insurance Corporation, the U.S. agency that promises to reimburse lost funds.

Unlike boring traditional institutions, the group argues that banking can be downright fun. “Play. Win big,” says Yotta, who features a lottery-like system that boosts profits for a few lucky customers.

This model is increasingly popular, especially among twenty- and thirty-somethings, and it is legal.

The problem is that while these startups may look and feel like banks, they aren’t. They simply take customers’ money and pass it through financial technology intermediaries like Synapse to old-school banks that may have only a physical branch and minimal online presence. The banks, including West Memphis, Ark.-based Evolve Bank & Trust, are the ones actually handling depositors’ money, according to the filing.

If any link in this sequence is broken, it could become extremely difficult for people to access their funds.

When it filed for bankruptcy in the spring, Synapse said it had only $2 million in cash and would owe exorbitant amounts for that amount.

Soon after, account holders at Juno, Yotta and others, with nearly $300 million in cumulative deposits and no direct relationship with Synapse, were no longer able to access their money.

The only one of the above teams that is actually a licensed bank, and therefore covered by FDIC insurance, is Evolve. And since Evolve itself did not go bankrupt, online lender customers were not eligible for automatic federal bank insurance.

“It’s really unprecedented,” said Jason Mikula, a former Goldman Sachs product manager who now writes a financial newsletter. “There’s no direct legal authority for the FDIC or any other agency to intervene.”

The companies involved point the finger at each other. Yotta, who repeatedly advertised its products as “FDIC-insured,” told customers it couldn’t help them because it didn’t have any of the money in its pocket. Synapse founder Sankaet Pathak blamed Evolve, write in a Medium post that it was “unnecessary and punitive” for the bank to freeze the funds. Neither Mr. Pathak nor representatives of Juno and Yieldstreet responded to requests for comment.

Yotta founder Adam Moelis, son of famed investment banker Ken Moelis, said he took responsibility for trying to fix the situation, but not for causing it: “The responsibility of the banks and Synapse was to store and move money and to have proper oversight.”

He added: “These are basic things. While we feel terrible about the impact this has had on our clients, the fact that these parties are unable to account for and reconcile tens of millions of dollars is not our fault.”

Even for experts, what happens next is unclear. While some of the $300 million frozen in bank accounts has been released to customers, according to filings in Synapse’s bankruptcy case, the defunct company’s court-appointed trustee told the court there’s a “deficit” of about $95 million in funds Synapse managed for creditors.

Thomas Holmes, a spokesman for Evolve, said that pending court orders, the bank was withholding $46 million in funds because it discovered “numerous significant discrepancies” in Synapse’s filings.

The bankruptcy judge said he suspects tens of millions of dollars will never be found, but he has no power to force regulators to intervene. “This is a very, very unusual situation,” Judge Martin R. Barash said at a hearing last week.

In this Möbius strip of blame remain the customers, whom these lending startups call “end users.” To have a chance of getting their money back, they first have to figure out who has it.

Many were told at one point that they had debit cards and accounts at Evolve, but have now discovered that another, unnamed bank had their money. Evolve’s Mr. Holmes said the bank “transferred all end-user funds” to other banks at Synapse’s request, but declined to identify them. “It’s complicated,” he wrote in an email Friday, declining to elaborate.

During interviews, customers were shocked to learn that they were not eligible for immediate federal insurance.

“To me, it all seemed like a normal bank,” said Erick Baum, 45, a computer science professional from Sacramento, who transferred about $30,000 of his savings from JPMorgan Chase to Yotta after hearing about it on a popular financial advice channel on YouTube.

Mark Hingle, a paramedic from Gretna, Louisiana, was angered that regulators wouldn’t step up even though they were so quick last year to help struggling lenders who turned to wealthy customers like Silicon Valley Bank and First Republic. In those cases, depositors gained access to their accounts within days after regulators held auctions of failed banks and distributed federal insurance funds.

“I didn’t play with this money,” said Mr. Hingle, 33, who has $60,000 tied up and said he couldn’t pay for back surgery without access to his savings. “I thought this was an FDIC-insured bank.”

Representatives for the FDIC and the Federal Reserve, the top banking regulator, declined to comment. An FDIC spokeswoman pointed to a letter the regulator sent to the bankruptcy trustee, saying it found Synapse’s collapse “deeply troubling” and had responded to more than 1,000 complaints and requests for information from those unable to access their funds.

At Synapse’s bankruptcy hearing last week, one depositor, who said she was on the verge of selling her home to pay bills, noted that she had filed dozens of requests for relief from the FDIC. The agency’s only response, she said, was a copy of answers to “Frequently Asked Questions.”

Another depositor said, “The FDIC has shifted the liability to the consumer.” A third had previously told the court he was thinking about harming himself.

Judge Barasch said he had no answers. He suggested that depositors could hire their own lawyers to sue the parties involved.

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