Polythiophenes are the most widely utilized semiconducting polymers in organic electronics, but they are scarcely exploited in photonics due to their high photo-induced absorption caused by interchain polaron pairs, which prevents the establishment of a window of net optical gain. Here we study the photophysics of poly(3-hexylthiophene) configured with different degrees of supramolecular ordering, spin-coated thin films and templated nanowires, and find marked differences in their optical properties. Transient absorption measurements evidence a partially-polarized stimulated emission band in the nanowire samples, in contrast with the photo-induced absorption band observed in spin-coated thin films. In combination with theoretical modeling, our experimental results reveal the origin of the primary photoexcitations dominating the dynamics for different supramolecular ordering, with singlet excitons in the nanostructured samples superseding the presence of polaron pairs, which are present in the disordered films. Our approach demonstrates a viable strategy to direct optical properties through structural control, and the observation of optical gain opens the possibility to the use of polythiophene nanostructures as building blocks of organic optical amplifiers and active photonic devices.