BNCT is a radiotherapeutic modality of high LET energy for different solid tumors as colorectal carcinoma (CRC). Although clinical outcomes show advantages of BNCT, tumor recurrence remains a common challenge. Previously we have described the double strand DNA damage response (DDR) produced by BNCT. TGF-β/SMAD pathway has been involved in maintaining genomic integrity. The aim of these studies was to evaluate the activation of the TGF-β/SMAD pathway, its interaction with the DDR pathway and the possible use of LY2109761 (Ly), a specific inhibitor of TGF-β receptor, as a radiosensitizer for BNCT. Six groups were performed in a human colon adenocarcinoma (HT29) cell line: NCT (neutrons), BNCT (boronophenylalanine plus neutrons), Control and the same three groups with the addition of Ly. The results showed an activation of the TGF-β/SMAD cascade with an increase in the genomic expression of TGF-β, SMAD7 and ATR (p < 0.001) at 2 h post neutron treatments compared to the Control group. A significant decrease in the expression of TGF-β receptor type I, SMAD7 and ATR for BNCT plus Ly was observed. Furthermore, it was demonstrated a decrease in tumor survival as a function of the total absorbed physical dose for all the treatments, being significantly higher in the groups treated with Ly at 1 and 3 Gy. On the other hand, a lower number of Ki67+ cells with the addition of Ly was found. Conclusion: The activation of the TGF-β/SMAD pathway and its interaction with the DNA repair via through ATR transductor was demonstrated. LY2109761 could act as a radiosensitizer for BNCT.