E4 series trains feature double-decker cars to accommodate additional commuter traffic around Tokyo and other urban areas.

[3] Sets P51 and P52, delivered in January and February 2001 were designed to cope with the steep gradients of the Nagano Shinkansen for use on services to Karuizawa.

[3] As with the earlier E1 series, the upper deck saloons of non-reserved cars 1 to 3 were arranged 3+3 with no individual armrests, and did not recline.

From 2014, the fleet of 24 sets still in service began to be repainted, receiving a new livery identical to that previously carried by the E1 series trains, with a toki (crested ibis) pink stripe separating the white on the upper body and blue on the lower body.

The first reliveried set, P5, was returned to service in early April 2014,[8] with the entire fleet be treated by the end of fiscal 2015.