Chipotle Mexican Grill shares soared in after-hours trade Tuesday after Bill Ackman's Pershing Square disclosed a 9.9 percent stake in the stock in a filing.

Chipotle stock last traded more than 5 percent higher in trading after the bell.

In a filing, activist investor Pershing said it intended to engage in discussions with the fast-casual restaurant company's board and management. It added the stock is undervalued and attractive.

Chipotle stock has been hammered by continued fallout stemming from food-borne illness breakouts that hit several restaurants locations across the country last year. Year to date, its shares are down 13 percent while the stock is off 45 percent from its all-time high hit last year.

For the first six months of this year, comparable restaurant sales, a key industry figure, dropped 26.5 percent as the chain continues to feel the lingering impact from the incidents, which were associated with restaurants in 15 different states.

To attract customers back, Chipotle has doubled down on promotions through a loyalty program and free food giveaways. It's also revamped its food-safety standards to try to prevent any food-borne illness in the future.

In a statement released after news of Pershing's stake in the company broke, a Chipotle spokesman said, "We welcome their investment, and appreciate the confidence they've expressed in our brand, differentiated offering, visionary leadership and strong growth opportunities."

Among Wall Street analysts, about half have a "hold" rating on the stock while a third rate it a "buy" or "overweight."

In an interview with CNBC, Stephen Anderson, a Maxim Group senior restaurant analyst, said the Ackman news did not change his opinion on the company. Since the food-borne illness outbreaks, "Chipotle's a fundamentally changed company with a different cost structure, a more restrictive cost structure." Anderson has a "sell" rating on the stock.

As the chain approaches future store openings with what management has described as "a more conservative lens," Anderson said he thinks the stock's multiple will have to come down to "more realistic" levels.