As a transition economy, Iran faces not only structural domestic challenges but also regional and global shocks. In recent years, the intensification of domestic, regional, and global uncertainties has become one of the major sources of instability in Iran’s agricultural trade. This issue highlights the necessity of examining its effects on trade flows in the agricultural sector from both economic policy and food security perspectives. The main objective of this study is to analyze the asymmetric effects of uncertainties on Iran’s agricultural exports and imports using the Nonlinear Autoregressive Distributed Lag (NARDL) model. The results reveal that increases in uncertainty, both in the short and long run, lead to a significant decline in Iran’s agricultural exports and imports. Moreover, the negative effect of rising uncertainty on trade reduction is stronger than the positive effect of its decline. The findings further indicate that Iran’s agricultural exports respond positively and significantly to the real exchange rate and the foreign income of destination countries, while agricultural imports respond negatively to the real exchange rate and positively to national income. Based on the results, several policy measures are proposed to mitigate the adverse effects of uncertainties, including diversification of export markets and import sources, development of insurance and risk-hedging instruments, strengthening domestic production of substitute products, improving logistics and infrastructure, and adopting stable exchange rate policies. Implementation of these strategies can enhance the resilience of Iran’s agricultural trade against domestic and external shocks.