The 68-year-old is the latest figure from Fifa's 'old guard' to step down from the organization.
Fifa said it would develop the work Dvorak had accomplished in its future drive for improvements, especially in his developments in the campaign to stamp out doping.
Dvorak is also a senior consultant in neurology at a Zurich clinic.
A series of directors at Fifa have left their posts since the election of Gianni Infantino at the head of world football's governing body in February.
Among them are Niclas Ericsson, the man in charge of TV rights sales, who has been at Fifa since 2003. The Swede will leave at the end of 2016.
Marketing chief Thierry Weil left in the the first week of October.
FIFA
Top doc becomes latest Fifa official to resign
Fifa's chief medical officer Jiri Dvorak on Wednesday stepped down from his post after 22 years in the job, football's world governing body announced.
Published: 3 November 2016 08:15 CET
Jiri Dvorak follows several other leading Fifa figures in stepping down. Photo: Nelson Almeida/AFP
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