Background: There is a significant amount of research which shows a proportion of girls are not engaging with physical education (PE) in school, resulting in a number of relatively inactive girls within the PE class. These girls are often identified in the literature as "low active", "hard to reach" or "disengaged". Reasons for this "disengagement" are often due to a combination of psychological, social and environmental barriers. Purpose: This research aimed to qualitatively explore the reasons for girls' disengagement in PE classes. By longitudinally tracking a sample of 'disengaged girls' from one case study school in Scotland, the study investigated if and how girls' experiences and engagement are affected by a physical activity (PA) intervention programme, "Fit for Girls". Research design: A questionnaire was used to identify five disengaged girls for three phases of semi-structured individual interviews. These were to track changes in girls' engagement and experiences in the PE environment. Interviews were carried out with the selected girls over an 18-month period, resulting in 15 interviews for this case study school. Data analysis: In order to understand why some girls have more positive PE experiences of a PA intervention than others, self-determination theory (SDT) was used as the theoretical framework for this paper. SDT is a useful theoretical framework for the present study because it explains task engagement in relation to the characteristics and needs of the individual, as well as the environmental conditions in which the individual acts. The theory proposes that the quality of a learner's engagement and motivation in an activity is related to the way in which the environment satisfies three main psychological needs: feelings of relatedness, competence and autonomy. Conclusions: Pre-intervention the PE environment did not fulfil the girl's basic psychological needs of autonomy, competence and relatedness. However, the PA intervention, which included consultation and a choice of activity, resulted in increased participation and more positive perceptions of the subject, for most of the selected girls. These factors resulted in a more supportive PE environment overall and so were critical for the girls transition from disengagement to engagement.