Controlled studies on the effectiveness of inpatient psychotherapy with patients with personality disorders (PD) are rare. This study aims to compare 3-month short-term inpatient psychotherapy based on transactional analysis (STIP-TA) with other psychotherapies (OP) up to 36-month follow-up. PD patients treated with STIP-TA were matched with OP patients using the propensity score. The primary outcome measure was general psychiatric symptomatology; secondary outcomes were psychosocial functioning and quality of life. In 67 pairs of patients, both STIP-TA and OP showed large symptomatic and functional improvements. However, STIP-TA patients showed more symptomatic improvement at all time points compared to OP patients. At 36 months, 68% of STIP-TA patients were symptomatically recovered compared to 48% of OP patients. STIP-TA outperformed OP in terms of improvements in general psychiatric symptomatology and quality of life. Superiority of STIP-TA was most pronounced at 12-month follow-up, but remained intact over the course of the 3-year follow-up.