This study aims to evaluate the circadian and circannual variations in a panel of analytes in horse saliva that have been previously described as biomarkers related to stress and disease, in order to interpret them correctly when they are measured in this species. This panel of analytes integrated cortisol, salivary alpha-amylase (sAA), lipase (Lip), total esterase (TEA), butyrylcholinesterase (BChE), adenosine deaminase (ADA), γ-glutamyl transferase (gGT), creatine kinase (CK), urea, total bilirubin, total protein (TP), and phosphorus. These analytes were measured in saliva obtained from a population of five clinically healthy mares from 06:30 to 20:30, every 2 h over two consecutive days in two different photoperiod seasons, winter and spring. The temperature and relative humidity did not change between the two consecutive days sampled in each sampled season, and no thermal discomfort was observed. Changes throughout the course of the day were observed for cortisol, sAA, TEA, BChE, ADA, and CK. However, a circadian pattern was only observed for cortisol, TEA, BChE, ADA, and CK. Moreover, the values obtained for sAA, Lip, and BChE were significantly different between seasons, with different daily rhythms for cortisol, TEA, BChE, and ADA depending on the season. In conclusion, this pilot study indicates that the time of the day and the season influence salivary analytes in horses, showing a rhythmic pattern for cortisol, TEA, BChE, ADA, and CK. These factors should thus be taken into consideration for the interpretation of analytes in horse saliva.