The battle has upended decades of precedent in the city.
There had been controversy over whether to vote Lee in because just last week the board had a split vote over appointing her as mayor.
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Historically, San Mateo's mayor has been the council member with the most seniority. In years past, the vote has been largely ceremonial and adhered to the seniority guideline.
Lee is now the first Jewish and Asian woman to serve as San Mateo's mayor.
She's been on the council for three years, and has the most seniority on the council, as the other three members were all new to the board. Three of four council members are new to the board, except Lee.
Over 100 people went in-person or called in through Zoom to comment on the mayoral debate and the appointment of a fifth council member.
A strong majority of them urged the council to make Lee mayor immediately.
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"This year ahead is going to be one of learning and growing together and it's an incredibly rare occurrence to have so many new council members and as we transition to by-district elections, let's always remember to remain united in our service to the community by considering our needs and interests of San Mateo as a whole," Mayor Lee said after her appointment.
The council voted in Richard Hedges as the fifth council member, 3-1.
Cracks have emerged among members over issues such as housing, splitting the council two and two.
That's made the appointment of Hedges all the more important because he could potentially be seen as a tiebreaker for some of the city's biggest issues.