Background Though appropriate condom use is an effective and cost-efficient strategy for HIV prevention, its use is inconsistent among female sexual workers (FSWs). Evidence on the magnitude and the drivers of inconsistent condom use across studies among FSWs is limited in coverage and scope. This analysis aims to determine the prevalence and associated factors among FSWs in Ethiopia. Methods This analysis uses the data from a cross-sectional ‘National HIV and sexually transmitted infections. Bio-behavioral Survey’ conducted from December 2019 to May 2020 using a respondent driven sampling technique. Descriptive statistics and multilevel logistic regression models were used to summarize data and measure strength of association. Statistical significance was determined by using P-value less than 0.05 or 95% CI that didn’t include unity. Results Overall, 6,085 FSWs from 16 cities and towns participated in the study. Participants’ mean (SD) age was 26.4 (± 6.06). The prevalence of inconsistent condom use across the 16 cities/towns was 17.1% [95% CI (16.5, 17.8)]. Factors independently associated with inconsistent condom use were being married/cohabiting [AOR = 1.56; (95% CI (1.03, 2.23), moderate to severe depression [AOR = 1.43; 95% CI (1.13,1.82)], alcohol dependence [AOR = 1.56; 95% CI (1.06, 2.31)], any drug use [AOR = 1.43; 95% CI (1.14–1.79)], older age (35–59 years) [AOR = 1.29; 95% CI (1.01, 1.64)], sexual violence [AOR = 1.75; 95% CI (1.43, 2.16)], sex selling location change [AOR = 1.27; 95% CI (1.06, 1.51)], length of sex selling experience [AOR = 3.01; 95% CI (2.27, 3.99)], anal sex [AOR = 2.74; 95% CI (2.15, 3.5)], number of non-paying sexual partner [AOR = 1.77; 95% CI(1.48, 2.11)], sex selling experience more than two cities [AOR = 3.01;95% CI(2.27, 3.99)], rape or forced sex [AOR = 1.75; 95% CI (1.43, 1.55)], not having comprehensive HIV knowledge [AOR = 1.39; 95% CI (1.15, 1.68)], newly diagnosed HIV [AOR = 1.52; 95% CI (1.19, 1.95)], and lack of condom access at the workplace [AOR = 2.1; 95% CI (1.69, 2.67)]. Conclusion Prevalence of inconsistent condom use among FSWs was 17%. Factors independently associated with inconsistent condom use included marital and education status, depression, alcohol dependence, drug use, sexual violence, and increased number of nonpaying partners. Program and individual level interventions need to be considered to enhance consistent condom use among FSWs.