School climate is a highly relevant variable that is associated with a series of positive results. However, there are still few studies that have statistically modelled the simultaneous influence of structural variables at the school level on the individual perception of the school climate and identification. This study had two objectives: (1) Identify school climate and school identification profiles at the individual and school levels. (2) Relate school climate and school identification profiles to factors located at the individual and school levels. The participants were selected from a probabilistic and stratified sample, n = 2070 adolescents (40.6% men, 59.4% women), aged between 13 and 18 years (M = 14.64, SD = 0.718), from 28 secondary schools in Chile. The results allowed us to identify four clusters at the student level and two classes of school climate at the school level. The explanatory factors at the individual level were Cognitive engagement (p < 0.001), Academic Expectations (p < 0.001), Positive Attitude to Authority (p < 0.001) and Family Conflict (p < 0.001). The explanatory factor at the school level was the school vulnerability index (p = 0.031). Finally, the explanatory effects of factors at individual and school levels on school climate are theoretically discussed.