The effect of fluorine (F) on diffusion of boron (B) in silicon (Si) is investigated by secondary ion mass spectrometry of Si, B, and F diffusion using pre-amorphized natSi/28Si isotope multilayers that are co-implanted with B and F. By the presence of F, diffusion of B is suppressed while that of Si is enhanced. A quantitative analysis of the experimental results based on our diffusion model shows that the suppression of B diffusion is due to (1) Si interstitial undersaturation caused by the time-dependent formation and dissolution of F-vacancy (FV) clusters and (2) direct interaction between B and FV clusters. The model developed in this study enables an accurate simulation of B and Si diffusion in the presence of F in Si.