The move coincides with the recent announcement of plans to restructure the commission according to its new vision of "charity working at the heart of society".
The image, which is likely to be followed by several similar ones in colours such as orange, turquoise and pink, was chosen by an eight-strong taskforce of staff of various grades.
"When we tested it out, I've never seen people in the Charity Commission get excited in quite the same way," said Geraldine Peacock, chair of the commission. "It's something that is fun and which people are enjoying, especially since they feel they've been slapped around the gills a bit recently.
"In time there might be six or eight related logos to represent different aspects of the commission, but we thought it best to begin with something that suggests involvement, simplicity, getting alongside people and supporting them."
Antony Robbins, head of communications at the commission, added: "The old logo suggested authority, even authoritarianism, whereas this one is almost funky.
"We're saying that charity is working at the heart of society, and here we have the logo on the T-shirt next to the heart of the person."