Sobotka's deputy, Interior Minister Milan Chovanec, known for his strong anti-migrant stance, will take over the party.
Foreign Minister Lubomir Zaoralek will take responsibility for the Social Democrats' campaign in October's elections.
The Centrist ANO movement led by billionaire Andrej Babis that is part of the current coalition government is heavy favored to win the ballot.
Babis called Sobotka's decision today a "desperate" move.
Sobotka will keep his post of prime minister until the election. His center-left coalition government was sworn in in early 2014.
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