Idiopathic halitosis is occasionally encountered in clinical practice, yet with scarce reports. This work aimed to investigate its features and potential association with low-grade systemic inflammation (LGSI). This retrospective study reviewed idiopathic halitosis from 2469 halitosis patients and compared them with 63 healthy controls (HCs). Organoleptic score (OLS), exhaled volatile sulfur compounds (VSCs), serum inflammatory cytokines, and fractional exhaled nitric oxide (FeNO200) to indicate LGSI were determined. Totally, 54 (2.19%) idiopathic halitosis patients were identified and they were extraoral. Dimethyl sulfide (DMS) was found to be the primary exhaled VSC. Inflammatory cytokines were slightly elevated in 5.56% (3/54) of idiopathic halitosis compared to none of HCs (p = 0.095). FeNO200 was elevated in 79.63% (43/54) of idiopathic halitosis compared to none of HCs (p < 0.001), with a sensitivity of 79.63% and specificity of 100% for the diagnosis of idiopathic halitosis. The FeNO200 level had positive correlations with OLS (r = 0.871) and DMS level (r = 0.485). Idiopathic halitosis is a rare condition which is closely associated with LGSI and possibly caused by unexplored extraoral pathologies. FeNO200 is recommended for its diagnosis with a high diagnostic power.