A meta-analysis of flunixin plasma and urine concentrations in 65 horses across Japan, the USA, the UK, and Australia was conducted using a nonlinear mixed-effects population model (POP model). The objective of this study was to provide regulatory authorities responsible for international harmonization with a balanced synthesis of available data to facilitate decisions on appropriate screening limits for medication control. The dataset included 55 horses administered with a single dose of flunixin meglumine (1.1 mg/kg or 500 mg/horse), and 10 horses administered multiple doses (1.1 mg/kg every 24 h for 5 days). Irrelevant plasma concentration (IPC) and irrelevant urine concentration (IUC) were estimated to be 1.9 ng/mL and 70.2 ng/mL, respectively, with a typical urine-to-plasma ratio (Rss) of 35.9. Under the current International Federation of Horseracing Authorities (IFHA) screening limits (SL) (1 ng/mL for plasma; 100 ng/mL for urine), plasma exhibited longer detection times (DTs) than urine—up to 41.4 h after a single dose and 125.6 h after multiple doses. This mismatch arises because the ISL ratio (100) exceeds the observed Rss (35.9)— a mismatch that becomes more pronounced after multiple dosing due to the plasma ISL intersecting a slow terminal elimination phase. Increasing the current plasma ISL from 1 to 3 ng/mL—while keeping the current urine ISL at 100 ng/mL—could better align the plasma and urine DTs. As a limitation of this study, both Standardbred and Thoroughbred data were included, and further data collection is needed to fully ascertain potential breed-specific effects. Moreover, this POP model also enabled relatively accurate Bayesian estimation of individual withdrawal times (WT). Clinicians could apply this Bayesian approach to making informed WT recommendations for horses when sufficient data is available. While existing non-POP statistical models remain viable, they may require a more conservative approach to WT estimation than Bayesian methods.