As in many other countries, the outbreak of the COVID-19 pandemic, together with subsequent government containment measures, posed significant challenges to small-scale broiler production systems in Egypt. Based on a survey of 205 specialist small-scale commercial broiler farms (SCBFs) consisting of both farm-based and household-based production systems, this study identifies the primary pathways through which COVID-19 has affected SCBFs and investigates the determinants of farm perception of these effects. A polychoric principal component analysis sorted the effects of the pandemic on the SCBFs surveyed into five categories, namely, input availability, production and operational costs, labor and human resources, consumer demand and sales, and farm finances. Next, five ordered logit models were constructed to examine the determinants of the SCBFs’ perception of each category of these effects. Generally, the empirical results revealed that COVID-19 affected SCBFs heterogeneously based on their management and production systems and resource endowment. Female-led and household-based SCBFs perceived significantly greater COVID-19 effects. In contrast, individually owned farms and those with membership of poultry producer organizations and larger total asset values perceived fewer effects. In addition, SCBFs operating in both local and provincial markets were less likely to perceive negative effects from the pandemic on their broiler farming activities. Although the adoption of strict and immediate containment measures was essential for controlling the virus and protecting public health, our results indicate that policy responses to COVID-19 must consider the likely effects on small businesses such as SCBFs since disruptions to such socioeconomically important supply chains will intensify human suffering from the pandemic. Overall, our findings provide important implications for the formulation of effective strategies for mitigating the impact of COVID-19 on small-scale broiler production systems in Egypt and enhancing their preparedness and resilience to future pandemics, natural hazard risks, and market shocks.