The move marks the second shakeup in the agency’s executive suite in three years; Mr. Krause succeeded Brian Heffernan, who left in September 2002.
Mr. Krause was hired to revitalize the office, which had suffered client defections.
The most recent parting came when Northwestern Mutual, on the agency’s roster for six decades, moved its business earlier this summer to Omnicom Group’s Downtown Partners, Chicago.
Mr. Krause said he is leaving to spend more time with his family, including his daughter, who was diagnosed with cancer last year.
Before taking the JWT job, Mr. Krause was CEO of Publicis, New York. For more than a decade he led the Chicago office of Publicis, previously a satellite of Hal Riney & Partners. Prior to that, he was an executive at Leo Burnett, another Publicis Groupe network.