Refugees and asylum seekers are at a high risk of developing mental health disorders, especially depression and anxiety. The prevalence of these disorders in refugees and asylum seekers has been well-documented in cross-sectional studies, but it is impossible to track their course over time using this research design. Hence, this systematic review and meta-analysis used data from existing longitudinal studies to examine the course of depression and anxiety in refugees and asylum seekers in upper-middle and high-income countries. Longitudinal studies reporting depression and anxiety were systematically searched from seven databases (Ovid MEDLINE, Ovid EMBASE, Ovid CINAHL, Scopus, Web of Science, PsycINFO, and Google Scholar) and included studies that fulfilled the inclusion criteria and underwent Joanna Briggs Institute (JBI) quality assessment. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was used to report the findings. An estimated pooled prevalence of depression and anxiety across time points was reported using a random effect model with a 95% confidence interval. Cochran’s Q and I2 statistics were conducted to assess heterogeneity among included studies, while funnel plots and Eggers tests were used to assess publication bias. Twenty longitudinal studies for depression and eight longitudinal studies for anxiety were included in the final analysis. The pooled prevalence of depression and Anxiety at baseline was 23.14% (95% CI: 16.34, 29.94) and 25.33% (95% CI: 5.10, 45.57), respectively. After the baseline data collection, the pooled prevalence of depression and anxiety increased over time. Specifically, the prevalence of depression rose from 17.55% (95% CI: 6.66, 28.45) 1 year after baseline to 34.04% (95% CI: 15.45, 52.63) 3 years after baseline. Similarly, the pooled prevalence of anxiety increased from 14.96% (95% CI: 10.59, 29.33) at 1 year after baseline to 33.09% (95% CI: 26.96, 39.21) at 3 years after baseline. The prevalence of depression more than doubled over the course of 3 years, rising from 17.55% at the 1-year mark after baseline to 34.04% at the 3-year mark after baseline. Similarly, the prevalence of anxiety exhibited a significant increase from 14.96% at the 1-year mark after baseline to 33.09% at the 3-year follow-up. These findings underscore the importance of implementing early settlement interventions and designing targeted measures to mitigate the prevalence of anxiety and depression among refugees and asylum seekers.