Darrell Clarke issued the order on Friday.
It sets the election for Tuesday, November 8 to fill vacancies in the 7th and 9th districts.
There's been a series of recent resignations from council, because the city charter requires that anyone considering a run for a different office resign from the office they currently hold.
The 7th district was represented by Maria Quiñones Sánchez. The 9th district was represented by Cherelle Parker.
Both are said to be considering a run for mayor.
"The political parties in Philadelphia will nominate candidates to run in the November special elections, and those nominees will appear on the Election Day ballot. The winners will serve the remainder of the unexpired term," Clarke's office said in statement.
Jim Kenney's term as Mayor ends at the end of next year, and several council members will be running to succeed him.
Two other vacancies were created by the resignations of at-large council members Allan Domb and Derek Green. No decision has been made on whether to hold an election to fill those seats.