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Long-term investors need to look at Chipotle: Analyst

McDonald's Chipotle
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The release of first-quarter earnings has pushed Chipotle's stock price lower while rival McDonald's stock gained strongly.

Both fast food giants fell short of Wall Street estimates, but Chipotle's stock has been hit harder.

McDonald's stock was up 1.84 percent to $96.62 in mid-day while Chipotle's was down 6.39 percent to $647.33.

Senior research analyst at Piper Jaffray, Nicole Miller Regan, pointed that it was important to be careful around earnings as "these stocks are trading on sentiments more than they are on fundamentals."

"Investors that are living in the large cap world need to look at Chipotle," told CNBC's "Squawk on the Street" on Wednesday. (Tweet This)

Chipotle reported $1.09 billion in revenue, falling short of the $1.11 billion estimate by analysts. McDonald reported $5.96 billion in revenue and with adjusted earnings per share at $1.01, falling under the earnings per share estimate of $1.06.

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While Chipotle fell short of estimates for comparable store sales growth in the first quarter, it still maintains high comps, up 10.4 percent, while McDonald's same-store sales were down 2.3 percent globally.

Regarding Chipotle, Regan said that there were no worries when it came to the brand itself since the company has one of the best management team.

"Today would be a good day to hop in and buy the stock," said Regan to CNBC.

McDonald's stock is down about 1 percent compared to a 26 percent increase for Chipotle over one year.

In addition to poor performing restaurants, McDonald's has been engulfed in a food safety scandal in China last summer, which could have prepared investors for lower financial results.

"Clearly McDonald is trading up with the expectation that it could have been worse and it's not," said Regan.

Read MoreChipotle disappoints Street on key sales metric

With the recent appointment of Steve Easterbrook as chief executive officer, analysts are waiting for a clear and solid plan, according to Regan.

"We are still living the Don Thompson results at this point in time," said Regan. She added that changes to McDonald's menu will take 12 to 18 months to show results.

Correction: The chart in this story has been updated to reflect that first-quarter revenue for Chipotle was $1.09 billion and for McDonald's it was $5.96 billion.