The concept of the 209 series was to create a lower-cost, minimal lifespan train (approximately 15 years) that would be replaced rather than rebuilt when they became life-expired.

These sets differ noticeably from the other 209 series variants in having 2.95 m (9 ft 8 in) wide cars (compared to 2.87 m (9 ft 5 in) for earlier flat-sided stock), as well as LED destination indicators, replacing the earlier roller blind type.

Between 2006 and 2007, three more sets (513–515) were transferred to the Keihin–Tōhoku—Negishi Line to replace the prototype 209-900/910/920 series trains and renumbered 82–84.

[8] Three ten-car prototypes were built in 1992 for testing and passenger evaluation on the Keihin–Tōhoku—Negishi Line, initially classified as 901 series.

The three sets incorporated a number of different design features for evaluation, but were converted in 1994 to bring them in line with the full-production specifications.

[10] Car KuHa 209-901 from the original 901 series set A was stored at Nagano Works,[11] and later preserved at Tōkyō General Rolling Stock Center.

This was the original classification given to the prototype E231 series 10-car set delivered in October 1998, to test out the then-new insulated-gate bipolar transistor (IGBT) traction system and TIMS passenger information system.

Based on the 209-0 series, these trains have end doors for use in emergencies inside tunnels.

These are four- and six-car sets based at Makuhari Depot modified between 2009 and 2013 from former Keihin–Tōhoku—Negishi Line 209-0 series ten-car sets for use on Chiba area and Bōsō Peninsula local services from 1 October 2009 to replace ageing 211 series trains.

Modifications include new electrical equipment, the addition of transverse seating to end cars, LED destination indicator panels, and a toilet.

[21] Modifications include new electrical equipment and the addition of LED destination indicator panels.

Branded "B.B.Base" (an abbreviation for "Boso Bicycle Base"), it re-entered service on 6 January 2018.

[25] While visually similar to the original 209-0 sub-series, these sets differ in having passenger-operated door controls.

[12] Between February and March 2007, some of the previously sealed windows in each car were modified to allow them to be opened.

[28] However, they re-entered service and served as additional trains as the 209-3500 and E231-3000 series sets were modified for wanman driver-only operations.

[6] Between November 2020 and October 2021, the trains were modified for driver-only operation (wanman (ワンマン, "one man")).

The set is finished with pale yellow body stripes and bears the text "YOKOHAMA Training Center".

[citation needed] It replaced the existing 105 series two-car training set located there.

The set is finished with Shōnan green/orange body stripes and bears the text "TOKYO•OMIYA Training Center".

The set is finished with orange body stripes and bears the text "HACHIOJI Training Center".

[citation needed] It replaced the existing 115 series two-car training set located there.

Externally, it is finished with green body stripes on unpainted stainless steel.

The train is based at Kawagoe Depot and began testing on the Utsunomiya Line from November 2008.

[13] On 8 May 2020, at 3:55 pm, the front carriage of a local service (6-car set C612) derailed between Awa-Kamogawa and Awa-Amatsu stations.