Amorphous boron nitride (aBN) materials have similar density to crystalline phases and retain many unique electronic properties, valuable chemical inertness and high thermal stability characteristics. However, the current research on aBN materials has mainly focused on the synthesis and electrical properties of ultrathin aBN films. In this study, we developed a post-annealing assisted femtosecond laser deposition route towards stoichiometric, continuous, and multifunctional aBN films with thickness values of ∼1 μm. A series of boron nitride films were deposited on silicon wafers using a 1030 nm, 300 fs laser with a pulse energy of ∼1 mJ and a high repetition rate of 2 kHz to ablate a hexagonal boron nitride target. The deposited films were then annealed at 900 °C in a nitrogen atmosphere. The structures and chemical compositions of these obtained films were analysed by X-ray diffraction and X-ray photoelectron spectroscopy. Fourier transform infrared and nano-scratch tests were performed to measure the infrared optical and frictional properties of the adhered films. An infrared thermal imager was used to investigate the heat-dissipation performance of these films. The results indicate the components of the aBN film are further purified, the number of large heterogeneous particles is effectively reduced, and the surface becomes smooth after post-annealing treatment. This improvement promotes the transfer of heat flux and increases the transmittance in the mid-infrared light band. The significant effect mechanisms of the post-annealing treatment on the enhancement of the composition and multifunctional properties of aBN films prepared by the femtosecond pulsed laser were provided. The uniform coverage of the aBN films on the substrates, as well as the mid-infrared optical transparency and the protective performance are highly valuable and practical for infrared window protection applications.