Chondroitin sulfate-functionalized ultra-deformable liposomes (CS-ACE-UDFLs) were developed for dual action, enhanced skin penetration and CD44-receptor-mediated precise delivery of drug. Optimization of critical parameters such as lipid concentration, sonication time, and edge activator concentration executed by Box-Behnken design. DLS particle size analyzer revealed nano-vesicle size (229.6 ± 7.95 nm), stable negative zeta potential (-41.30 ± 1.80 mV), high entrapment efficiency (73.53 ± 1.27%), and a low polydispersity index (0.253 ± 0.014) for CS-ACE-UDFLs. The encapsulation of aceclofenac confirmed through differential scanning calorimetry and X-ray diffraction studies. Surface characterization of CS-ACE-UDFLs with TEM analysis revealed a spherical morphology with a distinct chondroitin sulfate coating on the vesicle surface. In vitro release kinetics depicted the Korsmeyer-Peppas model, implying a complex release pattern, resulting from coupling of diffusion processes and matrix relaxation mechanisms. Enhanced drug release reported for CS-ACE-UDFLs (56.04% in 4 h, 91.80% in 8 h) post-incorporation edge activator compared to conventional liposomes (35.54% in 4 h, 68.51% in 8 h). The physicochemical parameters of CS-ACE-UDFLs were maintained during preliminary stability studies at 5°C. Confocal microscopy studies demonstrated a higher fluorescence intensity of functionalized ultradeformable liposomes hydrogel. Compared to ACE solution and ACE-UDFLs, CS-ACE-UDFLs showed superior anti-inflammatory activity in LPS-activated RAW 264.7 cells, characterized by enhanced cellular uptake and significantly lower levels of pro-inflammatory cytokines (IL-6, IL-1β, and TNF-α). In vivo studies on the CFA-induced arthritis rat model exhibited a significant reduction in paw volume and arthritis score (P < 0.0001) after treatment with the CS-ACE-UDFLs hydrogel system, indicating its potential in rheumatoid arthritis therapy.