The East African Community Common Market Protocol has led to improved cross-border labour migration in the region. The Protocol guarantees free movement and ensures workers are not discriminated against based on their nationality concerning employment, remunerations, and other conditions of work and employment. The Protocol however did not envisage the outbreak of pandemics and the attendant challenges. Available literature does not document and analyse how the functioning of border agencies addressed the needs and vulnerabilities of migrant workers and how that may have inadvertently led to abuses of their rights at the time of the outbreak. This chapter examined the extent to which the containment strategies in the region did not take into account the needs and vulnerabilities of cross-border truck drivers and how this may have led to the inadvertent abuse of their rights. The study was conducted in two East African countries; Kenya and Uganda and adopted a Human Rights to Development Approach. A descriptive analysis of the experiences of truck drivers crossing four border points was conducted. This chapter adds a voice to existing studies on the protection of migrant workers during pandemics and contributes to better migration governance within the East African Community.