Theoretical and experimental studies have highlighted the potential of surface-modified hexagonal boron nitride (hBN) flakes or boron nitride nanotubes (BNNTs) for achieving tunable electrical and magnetic properties. Here, we investigate the fluorination of BNNTs via a gas–solid phase reaction using molecular fluorine, focusing on controlling the degree of fluorination through varying reaction temperatures, gas mixing ratios, and reaction times. Effective fluorination is evident at elevated temperatures, with the degree of fluorination increasing with reaction time and temperature. Characterizations of the fluorinated BNNTs revealed fluorine incorporation, primarily on the outer nanotube layers, where fluorine preferentially binds to boron rather than nitrogen. Density functional theory calculations further indicate that fluorination becomes more thermodynamically favorable with increasing BNNT diameter and occurs preferentially at electron-deficient boron sites.