The No. 2 executive at Metro said Wednesday that he is leaving the transit agency after a six-year stint.

David Kubicek, the deputy general manager for operations, is resigning effective March 18. It will be the second high-level departure for the agency in coming weeks, and it’s unclear what Kubicek, 45, plans to do next.

Kubicek oversees Metrorail, the nation’s second-busiest subway system, as well as Metro’s capital projects and about 6,500 employees.

For riders, perhaps Kubicek’s most visable move was pushing for more rail-repair work to be done over weekends, which had the effect of trains running less frequently and led to some dips in ridership. But Metro said it helped to get more work done in non-rush-hour times.

He also was heavily involved in planning the new 7000 rail car series, opening a rail operations center in Landover and helping prepare for the opening of the Silver Line in Northern Virginia.

“He’s spent six years here, and he did a great job,” Metro General Manager Richard Sarles said.

Safety has been a persistent issue for the transit system in recent years, particularly since the 2009 Red Line crash, which killed nine people and exposed gaps in the transit agency’s safety practices.

Sarles said that Kubicek, who was in charge of Metrorail’s operations at the time of the Red Line crash, has been instrumental in making Metro safer.

“He’s helped strengthen the safety culture here, pushed escalator repairs and helped develop [a worker] protection program, all while dealing with the other daily things that come up.

“It’s six years of intense work, and he’s decided he’d like to move on and do something else,” he said.

Kubicek did not respond to an e-mail or phone call seeking comment. Sarles said he did not know what Kubicek’s next job plans involve.

The resignation comes as Metro is losing another of its top executives. Metro Transit Police Chief Michael A. Taborn is leaving in March after a 30-year career. Sarles is running a nationwide search for Taborn’s replacement.

Rob Troup, who runs the agency’s track, infrastructure and engineering services department, will serve as acting deputy general manager. Sarles said Troup is “certainly a person” he would consider to permanently fulfill the job. Troup has worked for Amtrak and as a consultant to New Jersey Transit — both employers also on Sarles’s résumé.

A Texas native, Kubicek was best known in his department for his attention to details and hard-driving personality. He would often brag of having walked all 100-plus miles of the rail system. He was also known for getting little sleep and for regularly working 12- to 14-hour days.

“He’s highly respected for his capability to understand issues and deal with issues,” said Peter Benjamin, a former chairman of Metro’s board. “He’s smart and understands the rail system.”

On weekends and nights, Kubicek would often show up at job sites unannounced — and in overalls with tools in his pockets — to check in on crews replacing track or other equipment. He would pass out gold pins that read, “Safety First.”

Kubicek was not without his critics. His staff, former board members and union representatives said that his sometimes-brash personality could be alienating and that his focus on operations sometimes came at the expense of attention to customer concerns and service.

He was an assistant general manager of rail operations in 2009 when the agency had its deadliest crash, with nine people killed aboard a Red Line train at Fort Totten. Four employees died in different incidents in 2009 and 2010 on the rail tracks.

More recently, Kubicek and Sarles have had to explain the mishandling of two incidents — one last summer and another in January. In both cases, stranded trains were improperly evacuated, with scores of passengers exiting trains on their own and walking along the tracks in search of refuge.

In 2011, Kubicek earned $240,000 a year and received an annual $30,000 housing allowance, part of the package he negotiated. His compensation for 2012 was not immediately available.

Kubicek came to Metro in 2007 as chief mechanical officer and was responsible for overseeing the maintenance, design and procurement of rail cars. Previously, he worked for the Los Angeles County Metropolitan Transportation Authority and the Dallas Area Rapid Transit agency, where he worked his way up from technician to senior manager of rail fleet services.

Jennifer Jenkins contributed to this report.