The strike was made by a US ally, Gen David Perkins told a military symposium.
"That quadcopter that cost 200 bucks from Amazon.com did not stand a chance against a Patriot," he said.
Patriots are radar-targeted weapons more commonly used to shoot down enemy aircraft and ballistic missiles.
"Now, that worked, they got it, OK, and we love Patriot missiles," the general said
However, Gen Perkins suggested deploying large surface-to-air missiles as a defence was probably not economically wise.
"I'm not sure that's a good economic exchange ratio," he told an audience at the Association of the United States Army's Global Force symposium in Alabama.
"In fact, if I'm the enemy, I'm thinking, 'Hey, I'm just gonna get on eBay and buy as many of these $300 quadcopters as I can and expend all the Patriot missiles out there'."