<p>The fragmentation of an economy through secession leads to a significant economic contraction. Specifically, secession is expected to severely impact food prices. This study examines the Sudanese economy, which faced profound consequences after South Sudan’s secession in July 2011. The economic effects of South Sudan’s secession remain underexplored, and this study aims to fill this gap by assessing its impact on food security, nine years post-secession. Using a Difference-in-Differences (DiD) with fixed effects, we quantify the effects of the secession. Moreover, to understand mechanisms driving the observed food price increases, mediation analysis has been conducted using the vegetable index and the number of violent events as mediator variables. Sudanese districts are considered the treatment group, while districts in neighboring countries—Kenya, Chad, and Ethiopia—serve as the control group. Synthetic DiD and Synthetic Control Method are employed as robustness checks. The consistent findings indicate that South Sudan’s secession led to around 72.00% increase in food prices in Sudan, threatening the country’s food security. This study provides an estimate of the economic consequences of secession on the food price index in a fragmented economy.</p>