This study provides a phytochemical characterization of Sambucus nigra L. (elderflower) and correlates its chemical profile with anti-inflammatory bioactivity, establishing an optimized extraction methodology. A comparative analysis of ultrasound-assisted extraction (UAE), accelerated solvent extraction (ASE), and shaking maceration was conducted using solvents of varying polarity (ethanol, ethanol–water mixture (1:1, v/v), and water). High-resolution fingerprinting via HPLC-ESI-QTOF-MS/MS confirmed a rich polyphenolic profile, dominated by flavonoids such as rutin, naringenin, and phenolic acids, notably chlorogenic acid. Quantitative analysis revealed that UAE with ethanol–water mixture (1:1, v/v) for 20 min yielded the highest recovery of rutin (4.87%) and chlorogenic acid (8.22%). The anti-inflammatory potential was evaluated in TNFα-stimulated HaCaT NF-κB Luc reporter keratinocytes. Anhydrous ethanolic extracts demonstrated superior efficacy, significantly inhibiting NF-κB pathway activation at non-cytotoxic concentrations. Chemometric analysis, specifically PLS-DA, identified naringenin as a principal contributor to this observed anti-inflammatory effect. These findings underscore the critical role of solvent selection in modulating the phytochemical composition and resultant bioefficacy of elderflower extracts. The potent, naringenin-driven inhibition of NF-κB in keratinocytes highlights the significant therapeutic potential of optimized S. nigra extracts for applications in dermatological and cosmetic formulations aimed at managing inflammatory skin disorders.