This study investigated differences in uterine and serum metabolome associated with clinical cure failure of metritis in dairy cows. Metritis was diagnosed in lactating Holstein cows from two Florida dairies and defined by the presence of fetid, watery, reddish-brown vaginal discharge from 4 to 12 days postpartum (dpp). Cows with metritis (n = 24) were paired with cows without metritis of similar parity and dpp (n = 24). On the day of metritis diagnosis (day 0), all cows with metritis received antimicrobial therapy. The continued presence of the fetid, watery, reddish-brown discharge on day 5 (n = 16) was defined as clinical cure failure, whereas clinical cure was defined by its absence (n = 8). Metabolome analyses of uterine lavage (days 0 and 5) and serum samples (day 0) were conducted using untargeted gas chromatography time-of-flight mass spectrometry. Normalized data were analyzed using partial least squares-discriminant analysis and ANOVA, adjusting P-values for multiple comparisons. Differences in the uterine metabolome on day 0 associated with clinical cure failure were linked to carbohydrate, amino acid, and lipid metabolism. Greater concentrations of arachidonic acid, ribose, and glutaric acid were associated with clinical cure failure, suggesting a greater degree of tissue lesion and inflammation. No differences in the serum metabolome were associated with cure failure. No differences in uterine metabolome were associated with clinical cure failure on day 5. The findings suggest that clinical cure failure is associated with a greater uterine inflammatory process that did not persist until cure assessment day.