This study reported proton therapy was associated with lower estimated secondary cancer rates compared to photon therapy in head-and-neck cancer patients. Based on data from 20 patients with head and neck cancer, a photon and a proton plan were developed for each patient. For proton therapy, six different variable RBEs in addition to RBE of 1.1 were used for secondary cancer rate calculation. Averaged across all patients and relevant organs, photon therapy compared to proton therapy with a constant RBE of 1.1 was estimated to be 1.8 times more likely to cause secondary cancer. This risk ratio varied between 1.6 and 2.0, depending on the variable RBE model used. Proton therapy was associated with lower rates of secondary cancer even when considering different variable RBE models to calculate the proton therapy dose distributions.