McCracken's resignation is effective July 1. A national search for a replacement will begin immediately, the letter said. No interim chief was appointed in the letter.
McCracken is the latest to resign in UNC leadership, joining former Chancellor Carol Folt, former UNC-system President Margaret Spellings and Vice Chancellor for Student Affairs Winston Crisp, among others.
In recent months, UNC Police has come under fire from all sides for the handling of protests regarding the Confederate monument Silent Sam. An independent report released in February found "serious deficiencies" in how UNC Police and UNC administration handled the Aug. 20 protest which saw the Confederate monument toppled.
The report states that although McCracken initially recommended using bike rack barricades around Silent Sam on Aug. 20, internal miscommunication resulted in barricades not being used at the protest.
UNC police officers that were interviewed in the report said that they believed it would have been impossible to break through the rings of demonstrators without resorting to "extreme physical violence."
Meanwhile, many anti-Silent Sam activists have criticized McCracken and UNC Police for their treatment of demonstrators.
Smoke bombs, pepper foggers and bicycles have been used by police to control tensions at protests on McCorkle Place. With pro-Confederate groups receiving police escorts to and from the base of Silent Sam at several protests, some activists have accused UNC Police of choosing to protect pro-Confederate demonstrators.
Since becoming chief in 2007, McCracken has helped develop and implement the Alert Carolina system, established the emergency management director position and implemented regular safety drills as part of University-wide emergency preparedness measures, the University's letter said.
"Jeff's legacy is a safer Carolina, and the establishment of strong and lasting collaborative relationships with our neighboring communities and regional first responders," the letter said.