Malnutrition remains one of the most common causes of morbidity and mortality among children, particularly in Ethiopia. The present study aimed to assess determinants of severe acute malnutrition among children aged 6–59 months in the pastoral community of Liban District, Southeastern Ethiopia. A case–control study design was conducted on 89 cases and 177 controls from 1–30 December 2020. A simple random sampling technique was used to select study participants. Data collected using interviewer-administered structured questionnaire were used, and anthropometric measurements were done by standardised calibrated instruments to collect data. Data were entered into EPI data version 3.1 and then exported to SPSS version 25.0 software for analysis. All candidate variables with P < 0⋅25 in bivariate analysis were then entered into multivariable logistic regression. Associated factors were identified at P < 0⋅05 and 95 % CI. A total of 266 (89 cases and 177 controls) having a response rate of 96⋅6 % being underweight [adjusted odds ratio (AOR) = 11⋅8, 95 % CI 3⋅17, 43⋅89], illness previous 2 weeks (AOR = 3⋅47, 95 % confidence interval (CI) 1⋅34, 8⋅99), family member with malnutrition (AOR = 4⋅52, 95 % CI 1⋅45, 14⋅01), greater than five family size, (AOR = 5⋅33, 95 % CI 2⋅08, 13⋅66), mothers unable to read and write (AOR = 3⋅66, 95 % CI 1⋅27, 10⋅56), mothers with low decision autonomy (AOR = 5⋅67, 95 % CI 2⋅26, 14⋅27), not handwashing at all critical time (AOR = 7⋅23, 95 % CI 2⋅74, 19⋅07), not feeding child animal source (AOR = 7⋅13, 95 % CI 1⋅98, 25⋅59), bottle feeding (AOR = 7⋅06, 95 % CI 2⋅34, 21⋅28) and being married (AOR = 0⋅05, 95 % CI 0⋅02, 0⋅19) were significantly associated with acute malnutrition. The present study has confirmed the association of acute malnutrition with maternal education, underweight, family size and inappropriate infant caring practices.