How to prescribe doses in boron neutron capture therapy (BNCT) remains controversial. Dose components in BNCT should be prescribed so that their biological effects are equivalent to those produced by reference photon doses in conventional radiotherapy, for which the dose–effect relationship is well understood because of the very large body of accumulated data and experience. For too many years, the “equivalent” gamma dose has been obtained from the boron and neutron doses by multiplying them by fixed weighting factors and adding them together. This simple additive procedure has been proven erroneous; it significantly overestimates the dose given to the tumor and underestimates the dose to healthy tissue, giving rise to potentially hazardous situations. An alternative is the isoeffective approach, which accounts for the nonlinear relationship between the reference photon dose required to produce a given biological effect and the high- and intermediate-linear-energy-transfer BNCT dose components, namely the boron- and neutron-related doses, required to produce the same effect. Here, we review the current state of the art and provide further support for this approach. As an application of these concepts, we analyze the performance of the Buenos Aires BNCT beam shaping assembly, showing the important consequences of adopting the second alternative.