The first vehicles were delivered in an unlined DMU green ( some apparantly in a dark and slightly bluish green) with white cab dome and no whiskers, although these were soon added. Later vehicles had them from new. When the two-character headcode box was added the whiskers were moved slightly apart at the bottom to accommodate.

From about '63 the small yellow panels appeared and they were painted into Brunswick and lined.

From the late '60s vehicles were painted into plain Rail Blue livery, and vehicles so treated until '68 had small yellow panels, red buffer beam, umber underframe / bogies and white cab roof dome. From '68 this was simplified to full yellow ends, black buffer beams, solebars and bogies and roof coloured cab domes.

When refurbished sets received all over white relieved by a twelve inch deep rail blue band below the side windows running the length of the vehicle, the inner ends of vehicles were rail blue. The first Cardiff are set in this livery was C 346 (50858 / 59366 / 50911) in Jan. '76.

The new livery however did not last long as it was too difficult to keep clean, and was superseded around 1979 by blue and grey. Not all of the class 116 vehicles were refurbished, and a small number remained rail blue well into the 1980s, though by this date most cars whether refurbished or not were at least repainted blue and grey. By 1986 only one 3-car set remained in all over rail blue livery, this unit was made up of cars, 53867/59372/53920. Originally allocated to Plymouth carrying set number LA322, then moving to Cardiff, Stratford, Tyseley and finally Manchester Newton Heath by 1988, being scrapped later that year. 

The Scottish units were all eventually painted blue and grey and carried the Greater Glasgow double ‘G’ symbol and the branding, ‘Trans-Clyde’ on one side of each driving car.  Set numbers were also applied to these units initially this took the form of a black stencilled three digit number carried on the cab front similar to those on the WR, this had been the practice in southern Scotland since 1966.  These were subsequently revised to identify the vehicle class becoming six digits in the same way as the EMU vehicles operating in Scotland a set numbering system that was subsequently universally adopted on all regions.

The class survived long enough for some to receive NSE livery, including 53083 and 53820.