Suzanne Fortier will take the helm of the 192-year-old institution.
The university announced today that the scientist, teacher, and McGill alumnus will succeed Heather Munroe-Blum, starting in September.
Fortier is currently president of a federal government granting agency, the Natural Sciences and Engineering Research Council of Canada.
"I am proud to be invited to serve as the next Principal and Vice-Chancellor of McGill," Fortier said in a statement.
"Principal Munroe-Blum blazed a trail as McGill's first female Principal and as an exceptional leader, and it will be an honour to follow in her footsteps. McGill opened up a world of opportunities for me, and I look forward to working closely with the McGill community upon my arrival."
Her appointment comes on the same week that Meric Gertler was named president of the University of Toronto.
Both nominees come from within the respective ranks of their schools' alumni. Fortier was chosen after a year-long selection process that saw the university conduct external consultations.
The appointment comes on the heels of news that McGill has fallen farther behind the U of T in the Times Higher Education World Reputation Rankings, having slid six spots to 31st while the U of T remained steady at 16th in the 2013 rankings.
McGill has also been facing a challenge from some nationalist critics in Quebec who lately have been lobbying the provincial government to slash its funding.
They want the amount reduced to more closely reflect the population rate of mother-tongue anglos living in the province — instead of overall enrolment levels, which include many out-of-province students and francophones.
The government has given no indication that it might take such advice, which was recently laid out in a prominent newspaper column in Le Devoir and in a letter from academics at francophone universities.
Meanwhile, Fortier's appointment is a second major linguistic milestone for Montreal in recent months. Last fall, Michael Applebaum became the first Anglo mayor of the city in 100 years.
In a statement, Munroe-Blum described her successor as an "exceptional person" who has distinguished herself in a number of ways.
McGill has educated two prime ministers, 12 Supreme Court justices, several foreign leaders, Pulitzer Prize winners, Academy Award winners and eight Nobel laureates.
It also boasts having created the first Internet search engine and hosted the landmark research of physicist Ernest Rutherford.