Joko Widodo, a former furniture exporter who achieved political prominence as governor of the capital, Jakarta, won presidential elections in July.
He defeated a former general with links to the regime of ex-dictator Suharto.
Widodo replaces President Susilo Bambang Yudhoyono, who has served since 2004.
Kerry will head a delegation of senior US officials, including assistant secretary for East Asia, Daniel Russel. The Obama administration has cultivated a stronger US relationship with Indonesia as part of its effort to "rebalance" American foreign policy toward Asia. President Barack Obama, who lived in Indonesia as a child, visited the country twice during his first term.