There are up and down yards on either side of the main line, with the single-track Grain branch line entering from the north east.
The up yard (south of the main line) consists of 14 sidings and three through roads, with other ancillary sidings. The down yard (north of the main line) consists of 10 sidings and three through roads. Some sidings in the down yard have been taken up.
As part of Phase 1 of the Kent Coast Electrification Scheme, the yard at Hoo Junction had a simple overhead catenary system installed in 1959, to accommodate the Class 71 electric locomotives then brought into use. These were equipped with a pantograph to work off the catenary, intended to avoid the exposed third rail which could have added a danger for yard staff. Due to introduction of diesel-electric locomotives the catenary system had become redundant by 1975.
The yard re-marshals wagon traffic on the main line and from the branch. The majority of traffic is aggregate wagons, with steel strip carriers are also present. Infrastructure units and ballast trains also use the yard. Container traffic from Thamesport used to pass through but this flow ceased around 2014 when the larger container shipping lines started using Thames Gateway instead of Thamesport.