The settlement, to be paid to Japanese medical equipment provider Terumo Corporation, follows a 6.6 billion yen lawsuit filed in Tokyo last year.
Terumo held almost seven million shares in Olympus.
In a statement, Olympus said Terumo has agreed to dismiss its remaining claim against the company.
Olympus said it wanted to resolve the matter ‘swiftly’, in part to avoid the potential costs of a lengthy legal battle.