The company said it was in “advanced stages” of appointing a new chief executive and Mr Thompson will remain with the business until 31 October as part of the transition.
The former state-owned company was locked into a bitter dispute with employee members of the Communication Workers Union (CWU) which ended last month when an agreement on pay and employment terms was settled.
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Royal Mail boss admits parcels are prioritised over letters
The settlement of that dispute has been listed as a reason for Mr Thompson to leave now.
“The changes we have made, the infrastructure we have put in place, and the agreements negotiated with our trade unions mean that Royal Mail now has a chance to compete and grow,” he said.
“That is what I have always wanted, and it is now the right time to hand over to a new CEO to deliver the next stage of the company’s reinvention.”
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Mr Thompson took on the chief executive role just over two years ago in January 2021. Prior to his appointment he served as a non-executive director of the board since 2017.
He thanks his team for their support in what he acknowledged as a “difficult and important time of change”.
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Royal Mail is owned by International Distributions Services plc (IDS) who also own an Amsterdam-based logistics company General Logistics Systems.