Phillips, who had been executive vice president, replaces Michael J. Dee, who resigned from the positions he had held since 2006. Dee, 53, also stepped down as a board director.
In a news release, the company said Dee served the bank "during a very difficult period" and that he would remain employed with the bank during a transitional period.
John M. Wright, senior vice president and chief financial officer, said the company would not say why Dee resigned, although he said it had nothing to do with regulatory action against the company last year.
In October, the Federal Reserve announced that Patapsco had reached an agreement with regulators on steps to maintain the financial soundness of the company and its Patapsco Bank subsidiary. That included improving the bank's earnings, strengthening board oversight of operations and reducing problem assets.
Dee had been chief financial officer at Patapsco in 2006 when he was tapped to replace CEO Joseph Bouffard, who left to head up BCSB Bancorp, the parent of Baltimore County Savings Bank. A Pennsylvania-based institution announced in June that it was acquiring BCSB.
Dee could not be reached for comment Monday.
Phillips, 57, declined to comment on Dee's resignation. The new CEO has been with Patapsco three years.
Chairman Thomas P. O'Neill said in a statement that Phillips' "extensive experience in banking, including in particular his experience in lending, will help put us back on the road to long-term success."
Patapsco also reported Monday that it lost $512,000, or 26 cents per share, for the fourth quarter that ended June 30. That compares with a profit of $932,000, or 47 cents per share, a year ago. The company said the loss in the April-to-June period was affected by $465,000 set aside for potential loan losses.
Banking consultant Bert Ely wrote in an email that based on reports filed with the FDIC, the bank saw a fourth-quarter increase of $1.3 million in loans whose borrowers were behind on payments.
"That deterioration in loan quality caused the bank to increase its loan provision for the quarter, which in turn was the major driver of the loss the bank experienced during the quarter," Ely wrote. "That negative turn in the bank's finances may have contributed to Mr. Dee's resignation."
Phillips said the bank has made "vast improvements" in recent years on its nonperforming loans, and he described the quarter as a "blip in the road." He said no one should link one quarter's performance to the change in management.
For the full year, Patapsco earned $381,000, or 19 cents per share, compared with a loss of more than $2 million, or $1.02 per share, the year before.
The bank's assets totaled about $230.8 million at the end of June, down from $254.4 million a year earlier.
The company's stock Monday fell 40 cents, or nearly 12 percent, to $3 per share.