There is a growing need to implement modern technologies, such as digital twinning, to improve the efficiency of transport fleet maintenance processes and maintain the company's operational capacity at the required level. Therefore, the paper reviews the existing literature to present an up-to-date and content-relevant analysis in this field. The proposed methodology is a systematic literature review using the Primo multi-search tool following Preferred Reporting Items for Systematic Reviews and Meta-Analyzes (PRISMA) guidelines. The main inclusion criteria included the publication dates (studies published from 2012–2024) and studies published in English. This resulted in the selection of 201 of the most relevant papers in the area of investigation. Finally, selected articles in this review were categorized into seven groups: a) air transportation, b) railway transportation, c) land transportation (road), d) in-house logistics, e) water and intermodal transportation, f) supply chain operation, and g) other applications. One of the main advantages of the study is that the results are obtained from different scientific sources/databases thanks to using the multi-search tool. Moreover, a bibliometric analysis of the selected papers was performed. The results have led the authors to specify the main research problems and trends related to the analyzed area and to identify the main research gaps for future investigation from academic and engineering perspectives. In addition, based on the review results, a framework for DT in transportation system maintenance was developed. The study ends with conclusions and future research directions.