Robert Pitofsky, a member of the Federal Trade Commission since 1978, resigned yesterday, a move that will enable a Republican majority to take control of the controversial agency.

Pitofksy, whose term would have continued until Sept. 25, 1982, said he was leaving the commission to return to academic life. He had planned for some time to leave this September and noted yesterday that his departure now will make it easier for the agency to reorganize under a new chairman.

The FTC is being run by Acting Chairman David Clanton, but with Pitofsky's resignation, President Reagan will have an opportunity to name a chairman to a fixed term. Until the Pitofsky resignation, there could be no Republican majority on the FTC until the term of Commissioner Paul Dixon expired on June 30.

"There is some advantage in getting back to academic life sooner than latter," Pitofsky said in an interview yesterday. "Since it was going to happen in September, I wanted to get the resignation out of the way.

"It will change the political makeup [of the FTC], but it stuck me that it didn't make much difference. I don't think the commission is going to get organized until the chairmanship decision is made," he added.

The resignation comes at a pivotal time in the FTC's recent stormy history. The Reagan administration, after backing off from a proposal to shut down the FTC's Bureau of Competition, thus stripping the commission of its antitrust authority, is seeking to shut down the agency's 10 regional offices over a three-year period.

In particular, David Stockman, the director of the Office of Management and Budget, has been sharply critical of FTC activities, particularly on the antitrust front.