Recent evidence has demonstrated that amorphous mixed phases are ubiquitous within mesostructured polythiophene-fullerene mixtures. Nevertheless, the role of mixing within nanophases on charge transport of organic semiconductor mixtures is not fully understood. To this end, we have examined the electron mobility in amorphous blends of poly(3-hexylthiophene) and phenyl-C(61)-butyric acid methyl ester. Our studies reveal that the miscibility of the components strongly affects electron transport within blends. Immiscibility promotes efficient electron transport by promoting percolating pathways within organic semiconductor mixtures. As a consequence, partial miscibility may be important for efficient charge transport in polythiophene-fullerene mixtures and organic solar cell performance.