In this study, we use a topology optimization algorithm, developed at the CNRS LPSC, to design a heavy-water neutron moderator for a BNCT treatment unit. The solutions generated by this algorithm are compact yet succeed in limiting the exposure of patient’s healthy tissues to levels below recommended limits. They present subtle, original geometries inaccessible to standard design techniques. The versatility of this novel approach makes it possible to automate the moderator design, and fit it to the configuration of the BNCT unit considered, e.g. the neutron source and materials it uses or the room it occupies, as well as to the biological parameters of its patients, e.g. the volume and depth of the tumor to be treated or the characteristics of the targeted organs.