The film features a gay teenage character, Marcus, whose identity is portrayed with dignity and complexity. His storyline focuses on overcoming trauma and finding self-expression, with his sexuality handled empathetically as one aspect of his multifaceted character. The narrative avoids stereotypes, presenting an affirming depiction of an LGBTQ+ youth.

The film features a transgender boy, Alex, whose character arc explores his struggles with identity and an abusive father. The narrative portrays Alex with dignity and empathy, highlighting the external challenges he faces while also depicting affirming support from the facility staff. For instance, a staff member helps Alex get a haircut that aligns with his male identity, validating his experience.

Short Term 12 portrays the profound impact of dysfunctional biological families, highlighting the necessity of chosen family structures and supportive relationships for healing and growth. The narrative critiques harmful parental authority and celebrates the formation of new, nurturing bonds outside traditional family units.