ABSTRACT Out-of-school comprehensive sexuality education (CSE) programmes are viewed by UNFPA as important in empowering youth. These programmes may, however, be critiqued for, firstly, inadvertently equating empowerment with individual agency to the exclusion of social justice; and, secondly, using the word empowerment as a self-evident signifier. We propose that empowerment be conceptualised within a critical sexual and reproductive citizenship (CSRC) framework that draws on feminist and queer re-workings of the principles of citizenship. To operationalise this conceptualisation, we developed the Masizixhobise toolkit from the five key issues outlined in the CSRC framework. The aim of the toolkit is to aid in the design and refinement of theoretically embedded empowerment CSE programmes. In this paper, we demonstrate the use of the toolkit. To do so, we analyse the Partners in Sexual Health’s (PSH) Sexual and Reproductive Health and Rights facilitator’s manual. A template analysis was conducted on this manual using a priori of themes from the toolkit. We sift through the PSH manual’s alignments or misalignments with the CSRC framework and make recommendations for enhancing the empowerment components of the manual. This example may assist others in designing and refining theoretically embedded and socially just youth empowerment CSE programmes.