The objectives of the present study were (a) to evaluate the importance of climate-related variables in the vaccination patterns applied in sheep and goat farms in Greece and (b) to assess potential interactions between these factors and previously established important health management- and human resources-related factors applied in the farms. Vaccination patterns against chlamydial abortion, clostridial infections, contagious agalactia, contagious ecthyma, foot-rot, paratuberculosis, pneumonia or staphylococcal mastitis were assessed. Climatic variables (2010–2019 and 2018–2019) were obtained for 444 locations with small ruminant farms throughout Greece. Patterns of vaccine administration in the farms were obtained through interviews with farmers. The following nine outcomes were considered: ‘vaccination against chlamydial abortion’, ‘vaccination against clostridial infections’, ‘vaccination against contagious agalactia’, ‘vaccination against contagious ecthyma’, ‘vaccination against foot-rot’, ‘vaccination against paratuberculosis’, ‘vaccination against bacterial pneumonia’, ‘vaccination against staphylococcal mastitis’ and ‘total number of optional vaccines administered’. Univariable and multivariable analyses were first performed to establish associations of each of the above outcomes with climatic variables. Then, the same approach was employed to assess the importance of climatic variables against health management- and human resources-related factors in the administration of vaccines in the farms of the study. Climatic variables had a higher association with vaccinations against infections in sheep flocks (26 associations) than in goat herds (9 associations) (p = 0.002) and in farms with semi-extensive or extensive management (32 associations) than in farms with intensive or semi-intensive management (8 associations) (p < 0.0001). In 26 cases (38.8% of all analyses evaluated), the climatic variables overshadowed the management- and human resources-related variables assessed as significant predictors for vaccination. In most cases, these referred to sheep flocks (nine cases) and farms with semi-extensive or extensive management (eight cases). For all eight infections, there were changes in the climatic variables found to be significant predictors from the 10-year dataset to the 2-year dataset. The results indicated that, in some cases, climate factors overshadowed factors traditionally considered for the formulation of vaccination programs. This points out the significance of taking into account climate conditions in the health management of small ruminant farms. Future studies can be focused on formulating vaccination programs in accordance with climate factors and also on setting the optimum season(s) for vaccination of animals based on the circulation of the pathogens, the risks for the development of diseases and the stage within the annual production cycle of the animals.