Primary school classrooms are foundational spaces that extend beyond academic learning to shape the overall development of young minds, influencing emotional, social, and psychological well-being. This study explores how various elements of the classroom environment affect pupil well-being in Nigerian primary schools, where increased access to education contrasts with poor classroom conditions such as overcrowding and inadequate infrastructure. Positive classroom environments, characterized by supportive relationships, constructive interactions, and stimulating physical settings, are associated with reduced anxiety, increased self-esteem, and improved academic performance. In contrast, negative environments can lead to behavioral problems, difficulties in concentration, and emotional distress. This study investigates the impact of three main aspects of the classroom environment—the physical environment, the social environment, and pedagogical practices—on pupil well-being. It aims to provide insights for educators, policymakers, and stakeholders to enhance classroom environments, thereby improving the quality of education and overall well-being of pupils in Nigerian primary schools. By understanding these dynamics, the study seeks to contribute to better learning outcomes, reduced behavioral issues, and a more fulfilling school experience for Nigerian children.