"We welcome their investment, and appreciate the confidence they've expressed in our brand, differentiated offering, visionary leadership and strong growth opportunities," Chipotle spokesman Chris Arnold told CNBC.
The investment is a validation that the burrito chain could bounce back after its series of foodborne illness outbreaks last year, according to three Wall Street analysts.
"This provides Chipotle with a prominent key shareholder, one that is likely to use its voice pro-actively," Mark Kalinowski, a Nomura analyst, wrote in a research note Wednesday.
However, the appearance of the activist investor may not be enough to spark a short-term turnaround for the company.
"We see no quick fix to what CMG really needs, a revitalization of top line, and activism's traditional tools for restaurants — spinoffs, refranchising, asset sales and cost cuts — don't appear to offer short-term opportunities, leaving few obvious quick levers to pull," Morgan Stanley analyst John Glass wrote in a research note Wednesday.
Still, he said, Ackman's investment could spur Chipotle to "hasten their turnaround efforts, which appear to have stalled."
The company received a boost from its Chiptopia program, which ends Sept. 30, during the second quarter, and the chain announcednew promotions last week that will run for the next month aimed at college students and families.
Glass noted that there are five potential activist moves for the restaurant chain: expanding its board, improving management's breadth of expertise, focusing on profit margins, curbing new unit expansion to increase cash flow and to either aggressively expand new food restaurant concepts or divest them altogether.
"The typical activist 'playbook' in restaurants has called for a combination of refranchising, cost-cutting and leverage," Credit Suisse analyst Jason West wrote in a research note Wednesday. "However, in our view, these options are less appealing in [Chipotle's] case given a high current valuation, lack of franchising historically, and since [Chipotle] would be selling stores that are significantly diminished relative to historic peak volumes and profits."
West said he expects Pershing to focus on improving the chain's sluggish sales.
"While CMG's sales recovery has been frustratingly slow and we see no silver bullets for a turnaround, Pershing's investment provides some validation of the long-term power of the brand," he wrote.