This is the first report in literature using hydrophilic interaction liquid chromatography (HILIC) in combination with diode array detector (DAD) for stability indicating determination of 5-Fluorouracil (5-FU) from its bulk form, pharmaceutical preparations, developed solid lipid nanoparticle (SLN) and nano structured lipid carrier (NLC) drug delivery systems as well as the rat skin extracts. The separation was performed at 45 °C, on Sequant Zic HILIC (250 mm × 4.60 mm ID, 5 μm, 200 Ao), peek HPLC column. Mobile phase is consisting of a mixture of acetonitrile: buffer containing 5 mM ammonium acetate (95:5; v/v). The pH of the mobile phase was adjusted to 7.0 using 1 M NaOH. The analysis was carried out at 0.75 mL min−1 flow rate with a detection wavelength of 265 nm and the injection volume was arranged as 10 μL. The developed method was fully validated in accordance with the International Council on Harmonization (ICH) Guidelines. Specificity of this method was demonstrated by forced degradation studies. As a result of calibration studies, the calibration curve was found linear in the concentration range of 1–250 μg mL−1 (R2 = 0.999). The precision of this technique calculated within the frame of intra-day and inter-day based on a percentage of relative standard deviation (RSD%) values (<2%). The limits of detection and quantification were 11 and 37 ng mL−1 respectively. On the other hand, 5-FU loaded SLN and NLC formulations with average particle size of 370 nm were also developed and compared in order to increase the permeation of drug into the rat skin. Ex-vivo Penetration/Permeation Studies indicated that higher dermal accumulation of 5-FU was obtained with NLC formulation. As a conclusion, the present work expressed the optimization and the validation of a selective, simple, precise and accurate fully validated HILIC method with sufficient sensitivity for the estimation of 5-FU in raw materials, marketed formulation and rat skin extract after applying both of the commercial product and newly developed nanoparticulate drug delivery systems on to the rat skins with high percentage recoveries.