The tradition of selling cookies goes back nearly a century and young scouts have typically been free to sell their cookies wherever they wish to as long as they are accompanied by their parents.
But some are now questioning whether there should be nationwide policies over where scouts are permitted to sell their baked goods.
"This is kind of a community issue," said Mike Lopes, a spokesman for the Girl Scouts of the USA.
"For the most part, it's not any different than selling in front of any other kind of shop. It just happens to be a marijuana dispensary."
The girl in San Diego was selling her cookies outside Urbn Leaf, which posted a photo of her on its Instagram account, sparking the heated debate.
"We were definitely surprised by the controversy this created," Will Senn, the founder of Urbn Leaf, told the New York Times.
"We all love Girl Scout cookies and thought a well-intended, lighthearted post to our social media accounts would be a little way to show our support," Mr. Senn added.
"While some have come out against her efforts due to the sales being made near a cannabis dispensary, there has been an outpouring of support from the public nationwide for this young entrepreneur and her creative marketing strategies.
"Why wouldn't we support a local girl's fund-raising activities?"
The young scout is not the first to employ the strategy.
In 2014, 13-year-old Danielle Lei sold 117 boxes in two hours outside a medical cannabis dispensary in San Francisco.
It prompted the Girl Scouts of Colorado to criticise Miss Lei and state that its branch rules banned scouts from selling cookies in front of marijuana shops, off-licenses or bars.
However, the organisation has since relaxed its policy and instead simply requires scouts to obtain prior approval from leaders.
