Background: Survival data for recurrent or treatment refractory pediatric atypical teratoid rhabdoid tumor (AT/RT), and its association to molecular groups is extremely limited. Methods: Single-institution retrospective study of sixty-four children <21 years old with AT/RT that was recurrent or refractory to frontline therapies (PD) treated at St. Jude Children’s Research Hospital from January 2000 to December 2020. Demographic, clinicopathologic, treatment, molecular grouping (SHH, TYR and MYC) and germline SMARCB1/SMARCA4 mutational data were collected. Progression-free survival (PFS2: time from initial PD to subsequent first progression) and overall survival (OSpostPD: time from PD to death/last follow up) were estimated by Kaplan–Meier analysis. Results: Median age at and time from initial diagnosis to PD were 2.1 years (range: 0.5-17.9 years) and 5.4 months (range: 0.5-125.6 months), respectively. Only 5/64 children (7.8%) are alive at median follow-up of 10.9 (range: 4.2-18.1) years from PD. The 2/5-year PFS2 and OSpostPD were 3.1% (±1.8%)/1.6% (±1.1%) and 20.3% (±4.8%)/7.3% (±3.5%), respectively. Children with TYR group (n=10) had a better OSpostPD compared to those with MYC (n=11) (2-year survival estimates: 60.0% ±14.3% vs. 18.2% ±9.5%; p=0.019), or those with SHH (n=21; 4.8% ±3.3%; p=0.014). In univariate analyses, OSpostPD was better with older age at diagnosis (p=0.037), female gender (p=0.008), and metastatic site of PD compared to local or combined sites of PD (p<0.001). Conclusions: Children with recurrent/refractory AT/RT have dismal outcomes. Older age at diagnosis, female gender, TYR group, and metastatic site of PD were associated with relatively longer survival in our study.