Background: Though prompt treatment seeking and effective treatment are important for controlling the transmission and elimination of malaria, there is no study done on delay in treatment seeking and its determinants among malaria patients in Shashogo District, a malaria endemic district in southern Ethiopia. Hence this study aimed to assess delay in treatment seeking and its determinants among malaria patients in health facilities of Shashogo District, Southern Ethiopia. Methods: A facility-based cross sectional study was conducted on 383 malaria patients proportionally recruited from all governmental health centers of Shashogo district, Southern Ethiopia from February 16- April 12, 2018. The data were collected using structured and interviewer administered questionnaires. Blood film test results were taken from the patients’ records. The data were entered in Epi-Data version 3.1 and analyzed using SPSS version 20. Multivariate logistic regression analyses was employed to identify the determinants of delay in seeking treatment. Odds ratios with 95% confidence interval (CIs) were computed to measure the strength of the association between the outcome and the explanatory variables. P-value ˂0.05 was considered as a statistically significant. Results: Of all participants, 284 (74.2%) of were delayed to seek treatment. Being illiterate (not attending education) (AOR [95% CI] =5.1 [1.16–22.74]), distance longer than 5 kilometer from the health center (AOR [95% CI] =2.52 [1.04–6.076]), poor malaria knowledge (AOR [95% CI] =2.48 [1.109–5.545]), negative attitude towards malaria (AOR [95% CI] =7.62 [3.37–17.22]), mothers involvement for the decision of treatment seeking (AOR [95% CI] =0.29 [0.091–0.937]) and unfriendly approach of health workers (AOR [95% CI] =2.85 [1.29–6.3]) were significantly associated with delay in seeking malaria treatment. Conclusion: Majority of malaria patients were delayed to seek treatment. Educational status, distance from the health facilities, knowledge, attitude, person involved in decision of malaria treatment seeking and approach of health workers were predictors of delay in seeking malaria treatment. There should be integrated advocacy, communication and social mobilization towards malaria.