Climate change-induced invasive pests remain a major bottleneck to agricultural productivity and food security in South Sudan. Strengthening the plant health system has the potential to contribute to reducing crop losses caused by pests. A situational analysis was conducted to assess the current state and effectiveness of plant health functions in three counties in South Sudan. Descriptive findings of data collected from 960 farmers in Juba, Yambio, and Yei indicated low access to plant health services, including advisory and extension, training, and information. There was a high dependence on NGOs and UN agencies to provide plant health services, indicating a gap in government-led initiatives. The findings demonstrate a complex relationship between plant health services and on-farm practices and regional variations in access to plant health services and resources. The findings have crucial implications for the plant health system in South Sudan, requiring the need for service accessibility, government involvement in plant health systems, strengthening of the policy and regulatory frameworks, and inclusivity in service provision.