The successful inclusion of students with special needs in physical education classes requires much planning and preparation. Lack of preparation of physical education teachers working in inclusive settings in Brazil has demonstrated the need for specialized training in strategies for implementing inclusion. The goal of this study was to identify, through self-reporting, common difficulties physical education teachers experienced while teaching children with special needs in inclusive environments. Two focus groups of physical education teachers who taught children with special needs were interviewed to provide data. Focus groups met twice for an average of two hours each meeting. An interview guide was employed to encourage discussion and idea sharing. Verbal interactions were transcribed and subjected to content analysis. Data analysis identified seven subthemes related to difficulties commonly experienced by the teachers working in inclusive environments: 1) access to diagnoses; 2) physical education syllabus; 3) inclusion and physical education; 4) architectural and administrative barriers; 5) family collaboration; 6) relationships with other professionals; 7) teacher training. Identifying these subthemes of commonly shared difficulties relating to successful inclusion may help guide the development of a training program for including students with special needs in physical education classes.