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There are various modes of transport available in Warrington.

Warrington has seven railway stations within its boundaries. The town has two main railway stations, Bank Quay on the London to Glasgow and Chester – Warrington – Newton le Willows – Manchester lines, and Central on the Liverpool – Widnes – Manchester line and the Transpennine route. Bank Quay is much altered, but Central (built 1873) is of some architectural merit, featuring polychromatic brickwork. However, both main railway stations have suffered from years of under investment. A new entrance and concourse has been built at Bank Quay, and similar work started in July 2010 at Central station. There are also stations in the suburbs at Warrington West, Sankey, Glazebrook, Padgate and Birchwood.

Warrington Bank Quay, to the south west of Warrington's town centre, is between Crewe and Preston on the West Coast Main Line from London Euston and Birmingham New Street to Glasgow and Edinburgh, with services operated by Avanti West Coast. There are also regional trains from Manchester to Chester and North Wales, from Chester to Leeds, and to Liverpool with one daily service to Ellesmere Port. Arpley and Walton Sidings nearby are a major rail freight interchange, and connect the main line to the freight line to Ditton Junction, which served Fiddlers Ferry Power Station until its closure, crossing the main line under Bank Quay station, where there were once low level platforms.

Central station has local services to Liverpool and Manchester and express services from Liverpool to Manchester then to Sheffield and beyond. The trains departing Central serve the urban rural fringe of Warrington and Manchester, serving Birchwood, Padgate, Irlam etc. before heading into Manchester. To the west, some trains serve Warrington West Station before heading into Merseyside and Liverpool. Beyond Manchester, the hourly East Midlands Railway train serves Manchester and then heads to Sheffield, Nottingham and Norwich. The station has an average daytime frequency of four trains per hour (three local trains operated by Northern and one fast train to Norwich (East Midlands Railway).

The River Mersey runs through the heart of the town dividing it into two. There are only two main thoroughfares crossing the Mersey in Warrington: at Bridgefoot and at the Kingsway Bridge. Another crossing is planned from Lower Walton to Arpley.

Warrington is also divided by the Manchester Ship Canal but there are three swing bridges and a high level cantilever bridge providing crossing points, and another high level crossing is planned between Warrington and Runcorn. The picturesque Bridgewater Canal runs through the Borough from the scenic village of Lymm to Walton Lea Gardens, a local park/leisure area. The first modern canal is also located in Warrington. The Sankey Canal starts at Spike Island in Widnes, going through Sankey Valley Park past Bewsey Old Hall & Gullivers World theme park, on through Earlestown and ending at the old Safeway store (now Tesco) in St. Helens.

Although Warrington itself does not have an airport, it is within half an hour (by road) of two international airports : Liverpool John Lennon Airport and Manchester Airport, each with a mix of various international, European, domestic and regional flights. You can reach Manchester Airport by train (via Piccadilly Station in Manchester). At one point Warrington was home to a world famous military airfield used intensively during World War Two at Burtonwood. Now the runway is part of the M62 and the area has now been transformed into Gemini business park. When driving down the M62 one can still see some of the old aircraft hangars that are now home to various businesses.

Warrington is home to the Warrington Cycle Campaign, a cycling advocacy group that has received international attention with its 'Cycle facility of the month' feature.