The 31-year-old clocked 1 minute 58.78 seconds in his semi-final at the Olympic Aquatics Stadium on Wednesday, to finish ahead of his US teammate Ryan Lochte by half a second, Xinhua news agency reported.
Brazil's Thiago Perreira was third quickest in 1:57.11.
Phelps, the most decorated Olympian in the history, has won each of his three finals in Rio so far, the 200m butterfly, the 4x100m freestyle and the 4x200m freestyle.
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