The COVID-19 pandemic caused unprecedented disruptions in the global economy, and container transport as a predominant means of the goods flow in global supply chains. Different measures employed worldwide to limit the virus spread, such as restrictions and quarantines on border crossings, port staff, container ships, transhipment terminals and the inland transport sector, created a colossal management challenge and caused a domino effect in delays. Consequently, it led to blank sailings and enormous rises in freight transport prices, the lack of supply reliability and shifts between different means of transport. These delays, enhanced by the Suez Canal blockage, exacerbated an already acute problem of the empty container shortage in the market. This paper aims to provide an in-depth overview of the COVID-19 pandemic’s impact on container transport and underline ways to increase resiliency against future disruptions. The research included a literature overview and formulation of recommendations. The paper contributes to the broad research of container transport management and provides insights for practitioners responsible for transport planning and disruption management.