Klebsiella pneumoniae is one of the major pathogens associated with multidrug resistance. This study aims to estimate the prevalence and characterize the molecular epidemiology of carbapenem-resistant K. pneumoniae in Thailand. We conducted a comprehensive search of PubMed, Embase, Scopus, ScienceDirect, and a Thai Journals Online (ThaiJO) from inception to November 19, 2024. Subgroup, meta-regression, and heterogeneity analyses were conducted. Publication bias was assessed using funnel plots and Egger’s test. The pooled prevalence estimates reflect proportions reported in published hospital-based studies. A total of 32 studies were included in the systematic review, with 27 studies included in the meta-analysis. The pooled proportion of carbapenem-resistant K. pneumoniae isolates was 87% (95% CI: 81%, 91%), with increasing trends observed for imipenem and meropenem resistance between 2014 and 2024. Ertapenem resistance remained high across regions, peaking in 2020 (100%) and 2024 (86%), particularly in the North and Northeast. The most prevalent carbapenemase gene was blaNDM (50%). Among the ESBL-associated genes, the pooled prevalence estimate was highest for blaCTX-M (86%). Co-harboring of blaNDM and blaOXA-48-like was observed in 36% of the isolates. Co-harboring of ESBL genes was detected in 25% of isolates. Subgroup and meta-regression analyses confirmed significant heterogeneity across regions and years. This meta-analysis highlights a high and growing burden of carbapenem-resistant K. pneumoniae in Thailand, marked by notable geographic variation and a predominance of blaNDM and ESBL genes. While the findings are indicative of important trends, the observed heterogeneity suggests that the results should be interpreted with caution.