Several strategies, including UV detection with a diode array detector (DAD), laser-induced fluorescence (LIF), derivatization reactions, the use of micelles in the separation buffer, as well as online preconcentration techniques based on pressure-assisted electrokinetic injection (PAEKI), and offline preconcentration using solid-phase extraction (SPE) columns containing quaternary amine groups with a chloride counterion, were investigated for the simultaneous separation and signal amplification of free thyroid hormones (THs) in biological samples. Moreover, a sensitive method for the quantification of THs in selected biological samples using micellar electrokinetic capillary chromatography with LIF detection (MEKC-LIF) was developed. The THs present in biological samples (L-tyrosine, T2, T3, rT3, T4, and DIT) were successfully separated in less than 10 min. The analytes were separated following a derivatization procedure with fluorescein isothiocyanate isomer I (FITC). A background electrolyte (BGE) composed of 20 mM sodium tetraborate (NaBO) and 20 mM sodium dodecyl sulphate (SDS) was employed. Key validation parameters such as linearity, precision, limits of detection (LOD), and limits of quantification (LOQ) were determined. The use of PAEKI for the electrophoretic determination of free THs demonstrates significant potential for monitoring these hormones in real urine samples due to its high sensitivity and efficiency.