Kennedy is situated at Eglinton Avenue, one block east of Kennedy Road, in Scarborough. The station is the current eastern terminus of Line 2, and the southern/western terminus of Line 3. Kennedy will also serve as the eastern terminus of Line 5 upon opening (projected 2022), and heavy construction is underway. Immediately east of the TTC station is the Uxbridge Subdivision and Kennedy GO station, owned by Metrolinx and served by the Stouffville GO Train Line.
Kennedy is a large complex arranged in four levels, on a primarily east-west axis. Line 2 serves the lowest underground level, which consists of one island platform. Trains pull into alternating sides via a scissors crossover west of the station, offloading and boarding from both sides. As two trains are commonly stopped at the platform simultaneously under this arrangement, digital signs at the bottoms of the stairs show passengers which train is due to depart next. Tail tracks east of the station permit storage for two trains. The overall atmosphere of the Line 2 platform level is dim and earthy, given the low ceilings and pervasive use of brown and orange tones in the tilework and trim.
Above the Line 2 platform is the underground station concourse, which contains washrooms, all three of the station's fare lines, and connects with all station exits. The concourse extends east and west from the visible station building, connecting to two western exits and one eastern exit. The eastern exit emerges as an open-air stairwell and elevator on the east side of the Uxbridge Sub near the original Kennedy GO station platform, and provides walking connections east along Eglinton Avenue. As of 2020 this area is undergoing construction to double-track the Uxbridge Sub, resulting in the demolition and replacement of the previous Kennedy GO station with two new side platforms. Potential modifications to the current TTC station exit to serve both new platforms are pending.
The two western TTC exits flank the east and west sides of nearby Transway Crescent. The east side exit consists of another open-air stairwell and elevator on the sidewalk, and serves as the main pickup point for passengers requiring the elevator. The west side exit is in the form of a passenger pickup and dropoff (PPUDO) island and circular indoor waiting room, ringed by a vehicle waiting loop. The waiting room is raised above grade by 3 steps like a stage, to provide a vantage point for passengers to identify their ride among a queue of waiting cars. A single staircase rises from concourse level into the middle of the waiting room; the entrance is not universally accessible.
Kennedy previously had a fourth, main exit facing north toward Eglinton Avenue, however this has been demolished for Line 5 construction, as the new platforms are situated immediately north of the original station box. The exit will be replaced with an above-ground headhouse as the new main entrance for the whole complex, and an expanded concourse linking the new Line 5 platforms with the existing station.
Above the concourse at ground level is the large bus terminal, serving 13 routes as of 2020. The terminal is within the fare paid zone, and consists of an indoor waiting area with a few retail kiosks, and outdoor sawtooth style platforms, all encircled by the bus roadway. The neighbouring GO station is at ground level, beside the bus roadway. Also at ground level are commuter park-and-ride lots (part of which have been disrupted by ongoing construction).
Elevated above the bus terminal is the Line 3 terminus, consisting of a single track flanked by platforms on both sides. This level is airy and bright, with window-lined walls and a clerestory vault over the track. The south side platform has been modified to extend out over a former second trackway, and provides elevator access. The north side platform is designated for offloading only (except for passengers requiring the elevator). This intended passenger flow is indicated by station signage; there is no physical barrier preventing contraflow traffic via the north side stairs, however the typically heavy unidirectional flow of customers on and off of trains is generally self-regulating.
All four levels are connected via a complex series of staircases, escalators, and elevators. Among these are two "express" escalators (one ascending and one descending) that connect directly between the bus terminal and the Line 2 platform two floors below, passing through the concourse level without stopping. Glass walls around the escalators prevent attempts to climb on or off midway.
Plans for the future Line 2 extension rejected repurposing the Line 3 alignment, instead calling for tunnels to continue eastward under Eglinton Avenue before turning north toward Scarborough Centre. The layout of Kennedy station was a factor in this decision, as the position and east-west orientation of the current Line 2 platform would prevent subway trains from turning sharply enough to join the north-south Line 3 alignment without digging a large, sweeping reverse curve under the neighbourhood to the northeast, or completely demolishing the station in favour of one at a gentler angle. The chronically low ridership of Line 3 stations between Kennedy and Scarborough Centre did not suggest that retaining the Line 3 alignment was worth the engineering challenges of either option.