Chipotle Mexican Grill has had its ups and downs in the last few years, but after its latest earnings report, it's clear that the chain is back with a vengeance, CNBC's Jim Cramer said Thursday after the stock surged 14 percent intraday.

With "colossal" same-store sales of 6.1 percent, healthy profit margins, rising digital orders and limited downside from higher labor costs, the fast-casual restaurant operator was able to wow Wall Street for two key reasons, Cramer argued.

The first is tied to Chipotle's new CEO, Brian Niccol, who replaced former CEO and founder Steve Ells last year after six years running Yum Brands' Taco Bell. In addition to addressing Chipotle's food safety concerns after a string of scandals, he helped speed up operations, introduced a loyalty program, put a lid on labor costs and started testing drive-through.

"I'm a big believer in Niccol's strategies — [...] the big-think redo of the chain as a place for dazzling innovation — and his tactics, which are all about good execution. He deserves plenty of praise for this run," Cramer said on "Mad Money."

This quarter, Chipotle's gross margins grew by a mind-blowing 210 basis points under Niccol's leadership. Paired with the higher same-store sales, but only a 2 percent boost in transaction prices, that suggests that people are "flocking back" to Chipotle's stores, Cramer said.

"Compare that to McDonald's. You know I like that stock — very well-run. But, nevertheless, it had a meager 2.3 percent same-store sales gain in the United States, and its gross margins actually declined by 190 basis points," he noted. "Chipotle's given you a remarkable turnaround here."

But Niccol's leadership isn't the only ingredient in Chipotle's newfound recipe for success.

"Father Time gets some credit, too," Cramer said. "The customers forgot about the health scares. Now they're back and they seem to love Chipotle, as I do, more than ever."

Over the years, Cramer has noticed a pattern with public companies that come across food safety issues. From Jack in the Box's infamous 1993 e-coli incident to Taco Bell's 2006 scare, it took around 18 months for their store traffic to bottom, then start to improve, he said Thursday.

In Chipotle's case, its journey from the stock's $250-a-share trough last year to its 52-week high of $606.00 on Thursday — a roughly 142 percent gain — was "a tour-de-force comeback" that was also "totally predictable," the "Mad Money" host said.

"You see, the American people tend to be very forgiving — or at least forgetful — when it comes to health scares, as long as you give them enough time," he said.

Shares of Chipotle ended trading at $585.78 on Thursday, up 11.35 percent. The stock has gained more than 115 percent in the last 12 months.