Background <p>Malaria constitutes a major public health burden in Sudan, accounting for most outpatient visits and hospital admissions across approximately 80% of the states. The armed conflict beginning in April 2023 severely disrupted an already fragile health system, affecting the surveillance system infrastructure. No prior studies have assessed the impact of conflict on routine malaria surveillance data reported through District Health Information Software 2 (DHIS2). This study evaluated the effects of conflict on completeness and reporting of malaria impact indicators data across Sudanese states.</p> Methods <p>A mixed-methods design combined quantitative analysis of quarterly DHIS2 data (January 2020–March 2025) from 17 states with qualitative exploration of surveillance system functionality. Quantitative analysis included descriptive analyses and interrupted time series analysis (ITSA) of three malaria impact indicators: quarterly reported malaria cases (presumed and confirmed) per 100,000 state population, test positivity rate (RDT + microscopy), and quarterly inpatient malaria deaths per 100,000 state population. Data completeness was quantified as the proportion of missing quarterly reports per state.</p> <p>Descriptive analysis graphs illustrate pre- and post-conflict trends and missing data patterns. ITSA was conducted for 11 states with complete post-conflict time series; six states with incomplete data were excluded. Three key informant interviews with national- and state-level malaria programme managers, selected from severe and less severe conflict-affected states, provided contextual insights. Qualitative data were analyzed using a deductive framework approach.</p> Results <p>Missing DHIS2 reporting increased substantially after April 2023. Inter-state variation was observed: western and southern states (except North Kordofan) experienced persistent data gaps, whereas northern and eastern states maintained relatively continuous reporting despite declining trends. Qualitative findings indicated stronger surveillance functionality in less-affected states by conflict. ITSA showed a statistically significant decline in quarterly reported malaria case rates per 100,000 state population at conflict quarter (p = 0.02), with no significant post-conflict trend change. Key informants identified health facility destruction, workforce shortages, unpaid salaries, and communication breakdowns as major barriers.</p> Conclusion <p>The conflict coincided with widening disparities in malaria surveillance across states, reflecting underlying inequalities in health system capacity. Strengthening states’ surveillance systems is critical in conflict-affected settings. Future research should examine locality-level impacts to better capture subnational variation.</p>