The city lies on a relatively high plateau on the northeast corner of the metropolis between the lowlands of Manila to the southwest and the Marikina River valley to the east. The southern portion is drained by the very narrow San Juan River and its tributaries to Pasig River, while running in the northern portions of the city is the equally narrow Tullahan River.

Quezon City is bordered by Manila to the southwest, by Caloocan City and Valenzuela City to the west and northwest. To the south lies San Juan and Mandaluyong City while Marikina City and Pasig City borders Quezon City to the southeast. To the north across Marilao River lies San Jose del Monte City in the province of Bulacan and to the east lies Rodriguez and San Mateo, both in the province of Rizal.

The city can be divided into a number of areas. The southern portion of the city is divided into a number of places including Diliman, Commonwealth, the Project areas, Cubao, Kamias, Kamuning, New Manila, San Francisco del Monte and Sta. Mesa Heights. The northern half of the city is often called Novaliches and contains the areas of Fairview and Lagro. Most of these areas have no defined boundaries and are primarily residential in nature.