Boston City Council elections were held on November 2, 1999. Eleven seats (seven district representatives and four at-large members) were contested in the general election, as the incumbents for districts 1 and 2 ran unopposed. Ten seats (six districts and the four at-large members) had also been contested in the preliminary election held on September 21, 1999.
Councillors Francis Roache, Stephen J. Murphy, and Peggy Davis-Mullen were re-elected. Councillor Dapper O'Neil, a member of the council since 1971, lost his seat to Michael F. Flaherty.
Councillor Paul Scapicchio ran unopposed and was re-elected.
Councillor James M. Kelly ran unopposed and was re-elected.
Councillor Maureen Feeney was re-elected.
Councillor Charles Yancey was re-elected.
Councillor Daniel F. Conley was re-elected.
Councillor Maura Hennigan was re-elected.
Councillor Gareth R. Saunders had announced in June 1999 that he would not seek re-election; his seat was won by Chuck Turner.
Councillor Thomas M. Keane Jr. had announced in March 1999 that he would not seek re-election; his seat was won by Michael P. Ross, who defeated Suzanne Iannella, daughter of former council president Christopher A. Iannella and sister of former council member Richard P. Iannella.
Councillor Brian Honan was re-elected.