Members of the public raised concerns about traffic, drainage and landscaping, but it was not enough to persuade the board to deny the permit.
The high school is the largest component of a $58.6 million bond referendum that voters approved earlier this year. Plans call for a facility with the capacity for 850 students.
Behind the building, the district plans on having at least one baseball field, a soccer field and tennis courts ready for athletes by the time the school opens. The city, which owns half of the land, will construct at least one baseball field and one softball field.
Constructing the high school will give St. Peter the flexibility to change grade configurations at other district campuses and free up classroom space to accommodate steadily growing enrollment.