ZnO thin films doped with iron have been grown by spray pyrolysis technique on glass and fused silica substrates in order to study the effect of substrate material on the structural, optical, and electro-magnetotransport properties of grown layers. The polycrystalline Fe:ZnO films have different growth orientation according to the substrate, though both films are highly transparent in the visible region of wavelength. The sample grown on glass substrate has larger magnetoresistance and lower electron mobility than that on fused silica substrate.