The fluorobenzene-ammonia van der Waals complex has been studied using a combination of two-color resonance enhanced multiphoton ionization (REMPI) spectroscopy, counterpoise corrected RICC2 ab initio molecular orbital calculations, and multidimensional Franck-Condon analysis. The experimental REMPI spectrum is characterized by a dominant, blueshifted band origin, and weak activity in intermolecular vibrational modes. RICC2 geometry optimizations and numerical vibrational frequency calculations of the neutral ground and first excited states have been performed on a number of different structural isomers of the complex using basis sets ranging from augmented double-zeta to quadruple-zeta level. Ground state basis set superposition error corrected zero-point binding energies show the in-plane sigma complex, forming a pseudo-six-membered ring connecting the fluorine atom and ortho-hydrogen, to be consistently the most stable of all six conformations considered, at all levels of theory. Comparison of computed zero-point excitation energies for the most stable pi and sigma conformers with fluorobenzene show that the sigma complex is the only conformer predicted to exhibit a spectral blueshift upon electronic excitation. The computed neutral ground and first excited state geometries and frequencies were used to perform multidimensional Franck-Condon simulations of the S(1)-S(0) vibronic spectrum for each of the most stable conformers. These simulations yielded null spectra for transitions involving the most stable of the pi complexes, pi(bridge); a spectrum rich in strong intermolecular vibrational structure for the second of the pi complexes, in complete contrast to the experimental spectrum; and for the sigma complex, a spectrum exhibiting weak intermolecular activity in line with that observed experimentally. This last simulation allowed an almost complete vibrational assignment of the intermolecular structure in the REMPI spectrum. The agreement between computational results and experiment overwhelmingly favors assignment of the spectrum to the in-plane sigma complex.