The announcement of Jim Samples' resignation came in an internal memo to Cartoon Network staff members.
"It's my hope that my decision allows us to put this chapter behind us and get back to our mission of delivering unrivaled original animated entertainment for consumers of all ages," said Samples, who was the network's general manager and executive vice president.
He said he regretted what had happened and felt "compelled to step down, effective immediately, in recognition of the gravity of the situation that occurred under my watch."
Dozens of blinking electronic devices showing a crude cartoon character had been planted in 10 cities as part of a guerrilla marketing campaign to promote the cartoon "Aqua Teen Hunger Force." But when Boston authorities got a series of calls about the devices on Jan. 31, they feared the circuit boards with wires could be explosives.
Cartoon Network's corporate parent acknowledged a few hours into the scare that the boards were harmless and part of a marketing move.
On Monday, Turner Broadcasting and an advertising agency involved agreed to pay $2 million in compensation for the emergency response the devices had spurred in Boston. The Cartoon Network is a division of Atlanta-based Turner Broadcasting, whose parent is media giant Time Warner Inc.
The agreement between Turner, Interference Inc. and several state and local agencies resolves any potential civil or criminal claims against the two companies.
Two men who authorities say were paid to place the devices in Boston have pleaded not guilty to placing a hoax device and disorderly conduct. Peter Berdovsky, 27, whose attorney has said also videotaped part of the police response, and Sean Stevens, 28, both are free on bond.
Boston police found 38 of the blinking signs on Boston's bridges, Fenway Park and at other high-profile spots. The magnetic lights, depicting crudely drawn "Aqua Teen" characters giving the finger, also were place in nine other U.S. cities for a publicity campaign, but they sparked a scare only in Boston. The small signs had apparently been up for two or three weeks in Boston before the calls to authorities last week.
Turner spokeswoman Shirley Powell said neither Samples nor Mark Lazarus, president of Turner Entertainment Group, would grant media interviews Friday.
Samples, 44, has not taken another job yet, Powell said. A replacement for Samples, who had been with the company for 13 years, was not immediately announced.
All the publicity over the marketing stunt didn't translate into much of a marketing boost for the show the network was trying to promote. The cartoon averaged 386,000 viewers last week among its targeted demographic of 18-to-24-year-olds, according to Nielsen Media Research. The previous week, the show averaged a virtually identical 380,000 among young viewers.