The League One club challenged the Premier League's decision to allow West Ham to play their home games at the venue after they were selected as preferred bidders by the London Legacy Development Corporation.
Orient were keen to relocate to the site in Stratford and the decision to allow West Ham to relocate from Upton Park led to concerns that fewer fans would attend matches at their current Brisbane Road stadium.
It was, however, revealed on Tuesday that an agreement has been reached between Orient and the Premier League to end the quarrel.
A statement on Orient's official website said: "The Premier League and Leyton Orient FC are pleased to announce that they have reached settlement of a dispute regarding the future use of the Olympic Stadium on terms which are confidential.
"Leyton Orient confirms, however, that it no longer disputes the validity of the Premier League’s decision to allow West Ham United to occupy the stadium."
West Ham are due to move into their new home ahead of the 2016-17 season.
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