Despite growing utilization of family planning in Ethiopia, many pregnancies in rural areas are still unintended and it remains the main global public and reproductive health challenges with devastating impact on women and child health and general public. Hence, this study was sought to determine the prevalence and associated factors of unintended pregnancy in rural women of Ethiopia. This study used the 2016 Ethiopian Demography and Health Survey data. Total weighted samples of 974 reproductive-aged rural women were included in the analysis. Multilevel mixed logistic regression analysis was employed to consider the effect of hierarchal nature of EDHS data by using stata version 14 to determine individual and community level factors. Variables significantly associated with unintended pregnancy were declared with adjusted odds ratio with 95% CI at p-value < 0.05. The prevalence of unintended pregnancy in rural women was 31.66%( 95%CI: 28.8%, 34.66%). Have no media exposure (AOR: 2.67, 95%CI: 1.48, 4.83), not working (AOR: 0.33, 95%CI: 0.21, 0.52), household size of one to three (AOR: 0.44 95%CI: 0.2, 0.96), primiparous (AOR: 0.41, 95%CI: 0.17, 0.99), poor women (AOR: 2.4, 95%CI: 1.24, 4.56), didn’t have intention to use contraceptive (AOR: 0.24, 95%CI: 0.14, 0.44) were individual factors associated to unintended pregnancy. Large central region (AOR: 4.2, 95%CI: 1.19, 14.62) and poor community level (AOR: 4.3, 95%CI: 1.85, 10.22) were community level factors associated to unintended pregnancy. The present study prevalence of unintended pregnancy in rural women was high. Maternal occupation, household size, media exposure, parity, women wealth, intention to use contraceptive, region and community level wealth were factors statistically associated with unintended pregnancy. Hence, demographer and public health practitioners give great emphasis to set strategies to increase accessibility women to media and improve women financial capacity, and strengthen availability of maternal health service to decrease unintended pregnancy adverse outcome in rural areas.