Clot-in-transit is associated with high mortality, but optimal management strategies remain uncertain. The aim of this study was to compare the outcomes of different treatment strategies in patients with clot-in-transit. This is a retrospective study of patients with documented clot-in-transit in the right heart on echocardiography across 2 institutions between January 2020 and October 2023. The primary outcome was a composite of in-hospital mortality, resuscitated cardiac arrest, or hemodynamic decompensation. Among 35 patients included in the study, 10 patients (28.6%) received anticoagulation alone and 2 patients (5.7%) received systemic thrombolysis, while 23 patients (65.7%) underwent catheter-based therapy (CBT; 22 mechanical thrombectomy and 1 catheter-directed thrombolysis). Over a median follow-up of 30 days, 9 patients (25.7%) experienced the primary composite outcome. Compared with anticoagulation alone, patients who received CBT or systemic thrombolysis had significantly lower rates of the primary composite outcome (12% versus 60%; log-rank P<0.001; hazard ratio, 0.13 [95% CI, 0.03-0.54]; P=0.005) including a lower rate of death (8% versus 50%; hazard ratio, 0.10 [95% CI, 0.02-0.55]; P=0.008), resuscitated cardiac arrest (4% versus 30%; hazard ratio, 0.12 [95% CI, 0.01-1.15]; P=0.067), or hemodynamic deterioration (4% versus 30%; hazard ratio, 0.12 [95% CI, 0.01-1.15]; P=0.067). In this study of CBT in patients with clot-in-transit, CBT or systemic thrombolysis was associated with a significantly lower rate of adverse clinical outcomes, including a lower rate of death compared with anticoagulation alone driven by the CBT group. CBT has the potential to improve outcomes. Further large-scale studies are needed to test these associations.