Two Cu(II) complexes of the non-steroidal anti-inflammatory drug Naproxen were synthesized, characterized and evaluated for anti-inflammatory, analgesic, ulcerogenic and urease inhibition activities. The complex 1 [Cu(nap)2(H2O)3]·H2O was reported previously, and the crystal structure of complex 2 [Cu(nap)2(dap)(H2O)] (nap = Naproxen, dap = 1,3-diaminopropane) was confirmed by X-ray diffraction crystallography. The anti-inflammatory and ulcerogenic study showed that the compounds 1 and 2 were the promising anti-inflammatory agents and demonstrated significant gastric tolerance when compared with Naproxen, especially for complex 1 with the edema inhibition of 93.6% after 3 h, and ulcer index of 15 ± 2. Analgesic and urease inhibition assay showed that complex 2 was a potent urease inhibitor with the IC50 value of 1.69 ± 0.08 μM and pain inhibition value of 65%. As effective urease inhibitors, molecular docking study was performed to investigate the binding mode of the complexes with urease.