Milligan, 35, had been the top administrator for the party organization for four years, taking over after the 2004 election.
It was unclear why Milligan was leaving. He notified central committee members Friday.
Milligan was seen as a skilled manager, having run the party aparatus through the 2006 election, but more importantly, the watershed 2008 presidential caucuses. Roughly 240,000 Iowans participated in the leadoff presidential nominating contest last year, almost doubling the previous high mark.