The M5 motorway to Bristol and Birmingham starts at Exeter, and connects at Bristol with the M4 to London and South Wales. The older A30 road provides a more direct route to London via the A303 and M3. The M5 is the modern lowest bridging point of the River Exe. Going westwards, the A38 connects Exeter to Plymouth and south east Cornwall, whilst the A30 continues via Okehampton to north and west Cornwall. Travel by car in the city is often difficult with regular jams centred on the Exe Bridges area. To address the problem, Devon County Council is considering the introduction of congestion charges.

Exeter's main operator of local buses is Stagecoach South West, which operates most of the services in the city. Dartline is a minor operator in the City. Former Cooks Coaches were taken over by Stagecoach forming Stagecoach South West. Western Greyhound is also a main operator connecting Exeter to Cornwall, Somerset and many different places in South West England. The High Street, pedestrianised except for bus and bicycle traffic, serves as the main hub for local buses. Country and express services operate from the city's bus station, in Paris Street, which intersects the High Street at its eastern end; some also call at Exeter St Davids railway station for direct connection to train services. Country bus services, mostly operated by Stagecoach, run from Exeter to most places in East and North Devon, but some are very infrequent. Regional express services run to Plymouth, Torbay, Bude, and along the Jurassic Coast to Lyme Regis and Weymouth, some operated by Stagecoach and others by First Bus. National Express operates long distance routes, for example to Heathrow and London.

There are two main line railway routes from Exeter to London, the faster route via Taunton to London Paddington and the slower West of England Main Line via Salisbury to London Waterloo. Another main line, the Cross-Country Route, links Exeter with Bristol, Birmingham, the Midlands, Leeds, Northern England, and Scotland. Many trains on all three lines continue westwards from Exeter, variously serving Torbay, Plymouth and Cornwall. Local branch lines run to Paignton (see Riviera Line), Exmouth (see Avocet Line) and Barnstaple (see Tarka Line). There is also a summer weekend service to Okehampton for access to Dartmoor. Exeter is served by two main railway stations. Exeter St Davids is served by all services, whilst Exeter Central is more convenient for the city centre but served only by local services and the main line route to London Waterloo. There are also six suburban stations, Topsham, St James Park, Exeter St Thomas, Polsloe Bridge, Pinhoe and Digby & Sowton, served only by local services.

Exeter International Airport lies east of the city and the local airline, previously called Jersey European and British European but now known as Flybe, is a significant local employer. The airport offers a range of scheduled flights to UK and Irish regional airports and charter flights including a seasonal service to Toronto, Canada. Connections to international hubs began with Paris Charles de Gaulle in 2005 and later a daily service to Amsterdam Schiphol Airport.