The emergence of COVID-19 in 2019 led the WHO to stipulate different containment measures. These measures were adopted by different countries to help limit and control the spread of the virus. The EAC Partner States developed regional and localized containment measures focused on the transport and logistics sector. The implementation of the measures, whilst contributing to the management of the spread of the virus, equally had negative effects to the sector as they affected the different sector players. It was, therefore, imperative to study the impact of the containment measures on transport and logistics and provide related policy recommendations in pursuit of sector competitiveness and trade facilitation.