The seven-member civilian board, which includes Toronto Mayor John Tory, voted Wednesday afternoon at police headquarters to keep Mukherjee in the position he has held since 2007.
Tory had been critical of Mukherjee in the past, but decided to vote him back in.
Mukherjee's previous one-year term saw calls for his resignation from the police union over a controversial image he posted to Facebook in December, with compared the numbers of Americans killed by police (more than 500) to the far smaller numbers of those killed by ISIS and Ebola. (Three and two, respectively.)
Mukherjee apologized for the post, but insisted he is the victim of a "smear campaign" by the union.
The year ahead will include contract negotiations and the search for a new police chief following the departure, in April, of Bill Blair.