The former Have I Got News For You host, who has acted before in comedies such as One Foot in the Grave and Nighty Night, will take on the role of George Windsor.
Deayton's character Mr Windsor is a modern languages teacher who is returning to school after travelling for a quieter life.
George Windsor's cynical attitudes towards education will be similar to those of veteran English teacher Grantly Budgen.
The 56-year-old will make his first appearance on the BBC serial in the spring of next year, from episode 27 of series eight.
The Deayton announcement comes soon after the casting of Daniela Nardini as an eccentric science teacher.
Waterloo Road returns to screens on Thursday, January 3 at 8pm on BBC One.
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