Eleven bilayer molecular junctions (MJs) consisting of two different 5–7 nm thick molecular layers between conducting contacts are investigated to determine how orbital energies and optical absorbance spectra of the oligomers affect the photocurrent (PC) response, the direction of photoinduced charge transport, and maximum response wavelength. Photometric sensitivity of 2 mA W−1 and a detection limit of 11 pW are demonstrated for MJs, yielding an internal quantum efficiency of 0.14 electrons per absorbed photon. For unbiased MJs, the PC tracks the absorption spectrum of the molecular layer, and is stable for >5 h of illumination. The organic/organic (O/O) interface between the molecular layers within bilayer MJs is the primary determinant of PC polarity, and the bilayer MJ mechanism is conceptually similar to that of a single O/O heterojunction studied in bilayers of much greater thickness. The charge transport direction of the 11 MJs is completely consistent with hole‐dominated transport of photogenerated carriers. For MJs illuminated while an external bias is applied, the PC greatly exceeds the dark current by factors of 102 to 105, depending on bias, bilayer structure, and wavelength. The bilayer MJs are amenable to flexible substrates, and may have applications as sensitive, wavelength‐specific photodetectors.