Fluxon dynamics in nonuniform Josephson junctions was studied both experimentally and theoretically. Two types of nonuniform junctions were considered: the first type had a nonuniform spatial distribution of critical and bias currents and the second had a temperature gradient applied along the junction. An analytical expression for the I-V curve in the presence of a temperature gradient or spatial nonuniformity was derived. It was shown that there is no static thermomagnetic Nernst effect due to Josephson fluxon motion despite the existence of a force pushing fluxons in the direction of smaller self-energy ͑from the cold to the hot end of the junction͒. A phenomenon, the ''zero crossing flux flow step'' ͑ZCFFS͒ with a nonzero voltage at a zero applied current, was observed in nonuniform long Josephson junctions. The phenomenon is due to the existence of a preferential direction for the Josephson vortex motion. ZCFFS's were observed at certain magnetic fields when the critical current in one direction but not the other becomes zero. Possible applications of nonuniform Josephson junctions in flux flow oscillators and as a superconducting diode are discussed.