John J. Casey, Braniff International's chairman the past two years, moved to Pan American World Airways yesterday to be executive vice president of operations.

Casey, 62, has served as Braniff's chairman during a most difficult period for the Dallas-based airline--when the financially strapped carrier had to convince employes to take pay cuts and make work-rule concessions and convince its 39 lenders to defer principal and interest payments on the airline's massive debt.

By moving from Braniff to Pan Am, Casey isn't taking a cushy executive suite position. Although Pan Am doesn't have the same problems in meeting its debt payments, it had operating losses of $348 million last year and has been seeking pay cuts and work rule concessions similar to those at Braniff.

However, it is expected that Casey at least will be paid in his new post. For about six months last year, he worked voluntarily without a salary.

Casey's departure ends a tough competition between brothers in the airline business. His brother, Albert, is chairman of American Airlines, which has been in a bitter competitive struggle with Braniff.

Braniff announced that its president, Howard D. Putnam, would succeed Casey.

Industry sources said Casey's move from Braniff was expected. Putnam, 44, recruited from the successful Southwest Airlines to join Braniff as president in September, has been "running the airline," a Braniff source said. In January, Putnam was named chief executive officer.

"But Casey's forte has been operations," his new area of responsibility at Pan Am, according to an industry source.

Putnam said yesterday that Casey's contributions to Braniff were "simply outstanding . . . Mr. Casey chose a new senior management team and turned the reins of the airline over to that team," he said. "Having done so, it is only natural for a person with his talents and energy to accept a new challenge."

In his new post at Pan Am, Casey will succeed James C. Waugh, who is retiring.