Due to their identification as third gender people, khwaja sira have historically been subjected to experiences of social marginalization. However, the extant literature has not fully explored the lived experiences of stigma and discrimination against khwaja sira in the Swat Valley of Khyber Pakhtunkhwa, Pakistan. To address this gap, we conducted 45 interviews with khwaja sira in Mingora, Swat, Khyber Pakhtunkhwa to better understand their experiences of gender-nonconformity stigma and discrimination in various social contexts, including within their families, in accessing health care, and within education and work contexts. Applying Minority Stress Theory and utilizing thematic content analysis, the present study identified three dimensions of gender-nonconformity stigma: (1) internalized stigma, namely feelings of shame and embarrassment; (2) perceived stigma, namely opinions others had of khwaja sira regarding lack of employability or engagement in sex work; and (3) enacted stigma, namely exclusion from families, in educational settings, in religious spaces, and in healthcare settings. Findings should inform future social intervention and community practice engagements with khwaja sira communities in Pakistan.