In a terse statement, the department store operator gave no reason for his immediate departure, effective Monday.
"We thank Michael for his hard work at J.C. Penney and wish him the best in his future endeavors," said Penney's CEO Ron Johnson.
Johnson, a former Apple (AAPL) Inc. executive who joined J.C. Penney in November, is trying to transform the department store chain from a retail has-been to retail darling.
The move comes as the department store chain is scrambling to reverse a sharp drop in customer counts and sales after a new pricing plan that eliminates hundreds of sales events ended up confusing customers.
Since announcing abysmal first-quarter results last month, Penney has been making changes to its advertising and marketing to better explain the three-tier pricing strategy that entails everyday low prices that are 40 percent lower than a year ago; monthlong sales that are deeper and are on select items; and clearance sale events.
But the company has also been backpedaling as well. It added five "Best Price Friday" sales throughout the year, which would be in addition to the sales it has on the first and third Friday of every month. The company is also resurrecting the word "sales" in its advertising, a word that was taboo under Johnson's original plan.
J.C. Penney hired Francis in October as president to redefine the Plano, Texas, company's brand and boost its business.
Francis was responsible for merchandising, marketing and product development, and was behind a monthly magazine that highlighted key items. The monthly issues resembled the cheap chic look from Target.
J.C. Penney has hired a number of big-name executives to help transform everything about the retailer, from the brands it carries to the store experience. The riskiest move was the elimination of hundreds of sales events in favor of more predictable low prices, but shoppers have not embraced the change.
Investors were spooked by Monday's announcement. Shares of J.C. Penney Co., which closed down more than 2 percent at $24.33, fell nearly 6 percent more in after-hours trading Monday on the news.
After Johnson laid out his vision for the new pricing strategy to analysts at the end of January, shares soared, peaking at $43.13 on Feb. 9. But they have lost almost half of their value since then.