The prevalence of people seeking care for Borderline Personality Disorder (BPD) in primary care is four to five times higher than in the general population. Therefore, general practitioners (GPs) are important sources of assessment, diagnosis, treatment, and care for these patients, as well as important providers of early intervention and long-term management for mental health and associated comorbidities. A thematic analysis of two focus groups with 12 GPs in South Australia (in discussion with 10 academic, clinical, and lived experience stakeholders) highlighted many challenges faced by GPs providing care to patients with BPD. Major themes were: (1) Challenges Surrounding Diagnosis of BPD; (2) Comorbidities and Clinical Complexity; (3) Difficulties with Patient Behaviour and the GP–Patient Relationship; and (4) Finding and Navigating Systems for Support. Health service pathways for this high-risk/high-need patient group are dependent on the quality of care that GPs provide, which is dependent on GPs’ capacity to identify and understand BPD. GPs also need to be supported sufficiently in order to develop the skills that are necessary to provide effective care for BPD patients. Systemic barriers and healthcare policy, to the extent that they dictate the organisation of primary care, are prominent structural factors obstructing GPs’ attempts to address multiple comorbidities for patients with BPD. Several strategies are suggested to support GPs supporting patients with BPD.