School climate is one of the significant factors determining educational achievement. However, the lack of instruments to measure it has complicated the study of this concept in Russia. We review the history of the study of the concept of “school climate,” and we discuss approaches to how it can be defined. We describe the most widely used questionnaires for studying school climate and analyze the set of components that have been included in them. To conduct the empirical study, we chose the student questionnaire that is used in the PISA international study, which provides a theoretical basis for measuring a number of dimensions of school climate. We conducted a psychometric analysis using methods from confirmatory factor analysis and modern test theory. It turned out that the structure of the indices that are used to measure school climate is not what the framers of the questionnaire assumed it would be. It is unclear whether the questions reflect the school climate indicators that are specifically proposed in the questionnaires. Some of the judgments in the questionnaire have been worded in such a way as to elicit most students’ agreement or disagreement with them without revealing any differences in how students perceive the subject of the question. The answer categories are unbalanced for most of the judgments. Respondents tended to fill them out in a one-sided fashion. We propose steps for how the instrument can be further improved.