Chipotle Mexican Grill's search for a new chief executive adds uncertainty to the restaurant's earnings trends, according to Blair, which downgraded the shares Thursday.
Even if Chipotle finds a new CEO quickly, the addition of a new leader often results in a costly few transition years, wrote William Blair analyst Sharon Zackfia.
"While ultimately the move may prove a positive over the long term and accelerate the company's turnaround, it also likely signals that trends remain under pressure and creates more near-term uncertainty until a successor is announced," she wrote Wednesday. "As a result, we are downgrading the stock to Market Perform."
Chipotle announced Wednesday that it has begun to search for a new CEO, with current chief and founder Steve Ells becoming executive chairman. Ells and two others are leading the search, the company said.
Chipotle shares rallied on the news of the leadership change and closed more than 5 percent higher Wednesday. Shares closed Thursday down 0.1 percent.
Foodborne illness outbreaks have plagued Chipotle. Most recently, a norovirus outbreak in July at a Sterling, Virginia, restaurant only pushed customers farther away. The company faced similar outbreaks during the past few years.
The company did not immediately respond to CNBC's request for comment on the analyst's downgrade.