Emanuel made the announcement at a press conference Monday morning.
"Garry began his career in the New York City Police Department where he rose through the ranks from patrolman to precinct commander to deputy commissioner," said Emanuel.
The mayor-elect also thanked Terry Hillard who has been the CPD's interim superintendent.
McCarthy has been head of the Newark Police Department since 2006. Prior to that, McCarthy also held a prominent post in the New York City Police Department.
McCarthy had been a candidate for the Chicago superintendent post in the past but he did not get the job.
The mayor-elect did not bow to pressure to appoint from within the Chicago Police Department's current ranks. Again, he looked east to another outsider who learned the basics of law enforcement on the other side of the Hudson River.
"I'd like to point out that the changes that we're going to create within the police department are going to come from within and build on the traditions that already exist here," said McCarthy.
The 52-year-old will follow Jody Weis, appointed by Mayor Daley in 2008. Under Weis' watch, reports of police abuse and corruption fell while the city's violent crime and homicide rates continued their downward trends. But Weis, an FBI agent, was never accepted by the police rank and file and was blamed for a morale problem.
"If you ask any police officer in this country they are going to say morale is low. The real question is, is morale improving or is it getting worse," said McCarthy.
The police union leader said the department's biggest problem is not morale but officer safety.
"The most important issue for police officers right now is the manpower levels. Right now, you have officers working in one-man cars which have historically been two-man units, and the backup is ten minutes away when it used to be two minutes away in certain neighborhoods," said Michael Shields, Fraternal Order of Police.
Emanuel will retain Robert Hoff as fire commissioner while naming federal homeland security deputy Gary Schenkel emergency management and communications director and educator Felicia Davis, a former police officer, as his public safety adviser.
McCarthy vowed to eliminate politics from police promotions and to support his officers when they are doing their jobs.
"As long as you're working hard and you're doing the right thing, I will have the cops' backs and they are going to learn that very quickly," he said.
McCarthy says he will attend the Chicago Police Academy and be certified as a police officer in Illinois before donning a uniform.
The city council must still approve Emanuel's choice.