Regulators said the fine was only 10 percent of his overall pay package.
While it draws a line under an episode some insiders had feared might cost him his job, Staley is the first sitting CEO of a major bank to face such a penalty.
Barclays had no immediate comment, but is expected to follow up on Friday by imposing a further fine of its own on Staley.
The regulatory findings will also be closely read by lawmakers keen to ensure top banking officials are held accountable for their actions at a time when there are growing calls to better protect whistleblowers.
The regulators stopped short of saying Staley was unfit to continue in his role, after he twice attempted to find out who wrote letters raising "concerns of a personal nature" about an unidentified senior employee.
"Mr Staley acted unreasonably in proceeding in this way and, in doing so, risked undermining confidence in Barclays' whistleblowing policy and the protections it afforded to whistleblowers," the FCA said.
Experts believe the fact the author of the letters was not a Barclays employee might have helped Staley's case, as there are strict rules designed to protect internal company whistleblowers.
Barclays had said in April last year it had reprimanded Staley and would cut his bonus as the two financial watchdogs launched a year-long investigation into his actions.
Authorities in the United States are still investigating the case.