VSK Manem and A Dhawan contributed equally to this article.Objective: We investigated the effects of conventional and hypofractionation protocols by modelling tumour control probability (TCP) and tumour recurrence time, and examined their impact on second cancer risks. The main objectives of this study include the following: (a) incorporate tumour recurrence time and second cancer risks into the TCP framework and analyse the effects of variable doses and (b) investigate an efficient protocol to reduce the risk of a secondary malignancy while maximizing disease-free survival and tumour control. Methods: A generalized mathematical formalism was developed that incorporated recurrence and second cancer risk models into the TCP dynamics. Results: Our results suggest that TCP and relapse time are almost identical for conventional and hypofractionated regimens; however, second cancer risks resulting from hypofractionation were reduced by 22% when compared with the second cancer risk associated with a conventional protocol. The hypofractionated regimen appears to be sensitive to dose escalation and the corresponding impact on tumour recurrence time and reduction in second cancer risks. The reduction in second cancer risks is approximately 20% when the dose is increased from 60 to 72 Gy in a hypofractionated protocol. Conclusion: Our results suggest that hypofractionation may be a more efficient regimen in the context of TCP, relapse time and second cancer risks. Overall, our study demonstrates the importance of including a second cancer risk model in designing an efficient radiation regimen. Advances in knowledge: The impact of various fractionation protocols on TCP and relapse in conjunction with second cancer risks is an important clinical question that is as yet unexplored Clinically, it is observed that over half of all cancer patients undergo radiotherapy over the course of their treatment, either as a primary treatment modality or in an adjuvant or a neoadjuvant context. In current radiotherapy treatments, tumours are often irradiated with a heterogeneous dose distribution throughout the treatment volume. The probability that all cancerous cells are removed from the system immediately post treatment is known as tumour control probability (TCP).1 The design and complexity of any treatment regimen in terms of improving therapeutic efficacy can be deduced (to some extent) from TCP values. Although a given heterogeneous dose distribution to the target volume locally controls the disease to a large extent (for a given radiation regimen), there are still shortcomings associated with the currently used radiation protocol. Of these, side effects are of great importance and can be classified based on the time to clinical presentation, with shorter-acting side effects arising from irritation of the skin or mucosa, or irradiation of tissues with sensitive adjacent structures. Late toxicities of radiation are known to manifest after a period of 10-15 years, and one of the major late toxicities is the appearance of a secondary...