This study focuses on examining the mental models of 11th and 12th-grade students attending a science high school in Turkey regarding the concept of the electron cloud. The study involved 72 students and employed the case study method. The precondition for selecting the sample was that the students had covered the unit on modern atomic theory in their chemistry classes. The concept of the electron cloud chosen for the study is integrated into the units of “Atom and Periodic System” and “Modern Atomic Theory.” To guide the research questions, the progression of the lessons and activities within the unit were observed in three-week intervals across different classes taught by the participating teacher. Research data were collected using a data collection tool consisting of 7 open-ended questions, considering the high school chemistry course objectives. The research questions were prepared in three categories: conceptual, relational, and visual. A rubric was developed for data analysis, and codes corresponding to levels of understanding were determined. At the end of the evaluation, three mental models were identified: the electron cloud model, the hybrid/synthesis electron cloud model, and the primitive model. For these models, eight mental model categories have been determined: fully scientific, partially scientific, conceptual, relational, conceptual–relational, conceptual-visual, relational-visual, and incompatible. At the conclusion of the study, only 5.56% of students provided answers at the scientific understanding level for all categories, placing them in the full scientific model category under the electron cloud model. 16.67% of students fell into the partial scientific model category, while 75.29% demonstrated a hybrid/synthesized electron cloud model. A small portion, 2.78%, adopted a primitive model.