The inclusion complexes of a new family of nonionic amphiphilic calix[4]arenes with the anti-inflammatory hydrophobic drugs naproxen (NAP) and ibuprofen (IBP) were investigated. The effects of the alkyl chain’s length and the inner core of calix[4]arenes on the interaction of the two drugs with the calix[4]arenes were explored. The inclusion complexes of Amphiphiles 1a–c with NAP and IBP increased the solubility of these drugs in aqueous media. The interaction of 1a–c with the drugs in aqueous media was investigated through fluorescence, molecular modeling, and 1H-NMR analysis. TEM studies further supported the formation of inclusion complexes. The length of lipophilic alkyl chains and the intrinsic cyclic nature of cailx[4]arene derivatives 1a–c were found to have a significant impact on the solubility of NAP and IBP in pure water.