Background: Left atrial appendage thrombus (LAAT) is the main cause of cardioembolism in patients with nonvalvular atrial fibrillation (AF). Emerging evidence indicates that direct oral anticoagulants (DOACs) may be a preferred, safer choice for patients with LAAT. However, current guidelines indicate vitamin K antagonist (VKA) as the preferred treatment for LAAT. We conducted a meta-analysis to compare the efficacy of VKA and DOAC for the treatment of LAAT. Methods: The search was conducted in the PubMed, Embase, Google Scholar, and Cochrane Library databases from inception to July 2022, with the language restricted to English. A first analysis was conducted to evaluate the risk of LAAT under VKA or DOAC treatment. A second analysis was conducted to compare the resolution of LAAT under VKA and DOAC treatment. Results: In 13 studies comparing LAAT incidence rates under VKA and DOAC treatment, significant superiority of DOAC was detected (pooled RR = 0.65, 95% CI = 0.47–0.90, p = 0.009) with moderate heterogeneity being identified in the pooled studies. In 13 studies comparing LAAT resolution under VKA and DOAC use, treatment with DOAC exhibited a significantly increased probability of LAAT resolution compared with VKA (pooled odds ratio = 1.52, 95% CI = 1.02–2.26, p = 0.040). Conclusions: This meta-analysis suggests a superiority of DOAC over VKA with respect to LAAT incidence in people with AF and the likelihood of LAAT resolution. Due to their established safety profile, DOAC is a preferable choice for anticoagulation, although further randomized controlled studies are warranted to provide further evidence of their suitability as a new recommended treatment.