Einhorn said the potential of the company's future products are being overvalued by other investors, such as a hospital collection service and patient record software offering.
For example, he said it's unlikely that hospitals will embrace outsourcing of their data to Athenahealth via its software, especially versus a competitor like Epic.
"Serious risks to the business model are being ignored," Einhorn said.
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A spokeswoman for Athenahealth did not immediately respond to a request for comment on Einhorn's presentation.
Einhorn said Athenahealth's health-care technology service business wasn't a bad one for its customers, but instead that its price had gone up far too much based on its real value.
"I am in no way rooting for it to fail," Einhorn said.
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Athenahealth has recently missed earnings targets and analysts have cut future revenue expectations, Einhorn said.
Still, the stock has moved up substantially in the last 12 months, on expectations the company would become a "national health information backbone for the United States of America," as company CEO Jonathan Bush put it.
The Sohn event, in its 19th year, features prominent money managers who present investment ideas free of charge to paying attendees. The money raised goes to fight pediatric cancer.
CORRECTION: Athenahealth's stock peaked in March 2014. The date was misstated in an earlier version.
—By CNBC's Lawrence Delevingne