Polyimide/hexagonal boron nitride (PI/BN) composite films have attracted interest as heat dissipation materials for advanced microelectronic devices. However, conventional preparations of PI/BN composite films employ harmful and expensive high-boiling organic solvents. In this work, thermally conductive PI/BN composite films were, for the first time, prepared using a nontoxic, eco-friendly, and inexpensive aqueous solvent. BN was ultrasonically exfoliated in a mixed solvent of water and tert-butanol to obtain aqueous BN suspensions, in which a poly(amic acid) salt (PAAS) was synthesized. The PAAS/BN suspensions were then drop-casted, and thermally imidized into PI/BN composite films. The PI/BN films exhibited excellent in-plane and out-of-plane thermal conductivities (up to 15.043 W/mK and 1.142 W/mK, respectively), which is attributed to the effective exfoliation and dispersion of BN in the aqueous solvent. Furthermore, these films exhibited high tensile strength, flexibility, and thermal stability.