Zootherapy, more specifically in its equine form, has proliferated recently as a therapeutic activity and is one of the most common applications in the stimulation of autistic individuals. At the same time, the influence of certain hormones was recently revealed in the behavior of autistic spectrum disorders. We propose to objectify the influence of analyzing equestrian therapies through laboratory methods and non-invasive techniques (salivary samples), in the hormone levels of cortisol and progesterone, thus indirectly those of oxytocin, before and after hippotherapy sessions for people with Autism Spectrum Disorder (ASD). The main results indicated that equine therapy decreased (p ≤ 0.05) the levels of salivary Cortisol in the rest of the sessions (before Hippotherapy 33.11 ± 0.96 ng/mL vs. after Hippotherapy 2.23 ± 0.75 ng/mL). And also the levels of salivary progesterone in the first session (before Hippotherapy 28.63 ± 12.81 ng/mL vs. after Hippotherapy 51.59 ± 33.11 ng/mL) and in the rest of the sessions (before hippotherapy 21.58 ± 12 pg/mL vs. after Hippotherapy 26.03 ± 11.98 pg/mL) which was always on the rise. These effective results were corroborated with the Cortisol/Progesterone Balance which reduced after equine therapy in the first session (before Hippotherapy 99.87 vs. after Hippotherapy 76.24) and the other sessions (before Hippotherapy 181.31 vs. after Hippotherapy 110.48). In conclusion, the Hippotherapy sessions for the population with ASD generated leads to an improvement in social attitudes, and it is confirmed with the effective modulation of the implicating hormones.