NEW YORK —

J.C. Penney’s largest investor and former board member, William Ackman of Pershing Square Capital Management, is selling his nearly 18 percent stake in the company.

The move to sell 39.1 million shares, announced in a regulatory filing late Monday afternoon, comes two weeks after Ackman resigned from Penney’s board as part of a deal to resolve an unusually public battle between the activist investor and the struggling department store operator.

The news sent Penney’s shares down nearly 3 percent to $13 per share in after hours-trading, after they closed down 15 cents to $13.35 in the regular session.

The latest development comes as the beleaguered chain is trying to recover from a transformation plan spearheaded by former CEO Ron Johnson that led to disastrous financial results.

Ackman resigned from the board on Aug. 13, after he went public with statements saying he’d lost confidence in Penney’s board and that Chairman Thomas Engibous should be replaced. Ackman and the retailer’s board also were bickering over how quickly the company should replace interim CEO Mike Ullman.