Background Infection in healthcare facilities is a major public health problem in most developing countries like Ethiopia. Currently the overall incidence of health care associated infection has been increased and burden of these infections is staggering. This study aimed to assess health care workers compliance with standard precaution practices and associated factors in public health institutions of Dawuro zone, south west Ethiopia, 2016. Methods An institution based cross sectional study was conducted from February1–30/ 2016 in 17 health institutions found in Dawuro zone. Data were collected using a pre-tested questionnaire on 250 health care workers selected by simple random sampling technique. Collected data was checked, coded and analyzed by using SPSS version 20. A P -value less than 0.05 was considered as statistically significant. Result Two hundred fifty health care workers were participated in the study. Out of the total respondents, 162(65.0%) of respondents had complied with standard precaution practices. Service year less than or equal to 5 years, training on standard precaution, having good hand hygiene and availability of personal protective equipment were independently associated with compliance to standard precaution practices. Conclusion Significant numbers of health care workers were not complied with standard precaution practices in this study. Therefore strategies targeted in fulfilling health institutions with supplies like hand hygiene material, Personal Protective equipment and training on standard precaution will improve compliance with standard precaution practice. Electronic supplementary material The online version of this article (10.1186/s12913-019-4172-4) contains supplementary material, which is available to authorized users.