Ce:Li6Y(BO3)3 (LYBO) is a well-known candidate for thermal neutron detection. So far, as-grown crystals exhibit a milky appearance that compromises their performance as scintillators. Current work demonstrates for the first time the growth of scattering-free LYBO by a thermal quenching process. The origin and features of the scattering centers are investigated in detail. Furthermore, the annealing treatment for the scintillation activation is studied, finding that the reduction in oxygen vacancies is mandatory. Under thermal neutron irradiation, the annealed scattering-free Ce:LYBO single crystal achieves a record-high light yield of 6200 ph/n in a single decay with a lifetime of 24 ns.