Deep reinforcement learning (DRL) is an emerging methodology that is transforming the way many complicated transportation decision-making problems are tackled. Researchers have been increasingly turning to this powerful learning-based methodology to solve challenging problems across transportation fields. While many promising applications have been reported in the literature, there remains a lack of comprehensive synthesis of the many DRL algorithms and their uses and adaptations. The objective of this paper is to fill this gap by conducting a comprehensive, synthesized review of DRL applications in transportation. We start by offering an overview of the DRL mathematical background, popular and promising DRL algorithms, and some highly effective DRL extensions. Building on this overview, a systematic investigation of about 150 DRL studies that have appeared in the transportation literature, divided into seven different categories, is performed. Building on this review, we continue to examine the applicability, strengths, shortcomings, and common and application-specific issues of DRL techniques with regard to their applications in transportation. In the end, we recommend directions for future research and present available resources for actually implementing DRL.