"It is a company that takes software and gives it to customers in exchange for solving complicated and expensive problems that they hate and stink at," he added.
Shares of Athenahealth have dropped nearly 15 percent as of Wednesday's close—two days after Einhorn's presentation at the Sohn Investment Conference in New York.
Einhorn is not the only one betting against Athenahealth.
Shares on loan—a common measure of short interest—is nearly 18 percent of outstanding stock, according to data tracker Markit. That's down from about 32 percent in March 2010, 35 percent in March 2012 and 22 percent in October 2013.
"If [the stock] drops and stays dropped, we will pay people there and then they'll get the upside from there," said Bush, who is paid in stock options. "Let the record show at $195 [a share]. I have to wait a while for my next million."
"But that's the point of paying CEOs in options," he continued. "If they don't deliver the value, the market doesn't see it, they shouldn't make any money. I'm OK with that."