Former high-flying hedge fund executive Arthur Samberg yesterday agreed to pay $28 million to settle insider-trading charges — closing a nearly-decade old probe that centered on the now-shuttered Pequot Capital Management.

The Securities and Exchange Commission said it will continue to press charges against David Zilkha, the Microsoft employee who allegedly passed on confidential information about the tech company’s earnings to Samberg in 2001.

Samberg hired Zilkha in early 2001 and then pumped him for “any tidbits” about the tech company’s earnings prior to leaving Microsoft, the SEC said.

Samberg’s funds earned $14 million tied to trades that predicted the stock would rise on the earnings news, which he learned from Zilkha, the SEC said. At the time, Wall Street had been predicting the software maker was going to miss its earnings targets, but it met them instead.

“I shouldn’t say this, but you have probably paid for yourself already,” Samberg said in an e-mail to Zilkha after he made the trades, the SEC said.

The SEC has been looking into Pequot’s trading since the early part of this decade, but the investigation hit roadblocks that overshadowed the case itself. One of the watchdog’s investigators claimed he was fired in September 2005 for ruffling too many feathers in connection with his investigation. That prompted a Congressional inquiry into the SEC’s handling of the case which led the SEC to reopen its failed investigation in 2008.

Last year, Samberg announced plans to shutter his firm due to the never-ending cloud of the SEC probe.