In this study, the level of fluoride in well and spring waters of selected woreda (district) of Jimma zone, Oromia Regional State, Southwest Ethiopia was investigated. Water samples were collected from Jimma, Serbo, Seka Chekorsa and Agaro towns in July, 2016. The collected water samples were stored at 4 °C until analysis. The fluoride content of water samples was determined using fluoride ion selective electrode (FISE). External calibration curve was employed in the range of 0.10–30 mg/L of fluoride standard solutions. The resulting calibration curve was exhibited good linearity with coefficient of determination (R2) 0.999. Satisfactory recoveries ranged from 79–120%, with standard deviation lower than 4.89 were obtained, indicating the validity of the employed method. Concentrations of fluoride in Jimma town well and spring waters were ranged from 0.19–17.73 mg/L and 0.18–0.25 mg/L, respectively. Whereas, the fluoride content of Serbo, Seka Chekorsa and Agaro well waters were ranging from 0.21–0.23 mg/L. The highest fluoride content (17.73 mg/L) was observed in well water of Jimma University. Except well water of Jimma University, the obtained fluoride content of all the studied water samples were below the WHO guideline (<1.5 mg/L) for drinking water. One way ANOVA test at p < 0.05 demonstrated the absence of significant difference in the fluoride content among the well waters of Serbo, Seka Chekorsa and Agaro. There was also no significant difference in the fluoride contents of spring waters collected from different area of Jimma town: Bacho Bore, Bossa Addis and Kochi.