A one-pot sequential Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) strategy is presented for the synthesis of constitutionally unsymmetrical cyclobis(paraquat-p-phenylene)-based rotaxanes in good yields from simple starting materials. The methodology consists of performing multiple CuAAC reactions to stopper a pseudorotaxane in a stepwise manner, the order of which is controlled through silyl-protection and Ag(I)-catalyzed deprotection of a terminal alkyne. The methodology is highlighted by the synthesis of an amphiphilic branched [4]rotaxane. The methodology increases the ability to access ever more complicated mechanically interlocked compounds to serve in devices as sophisticated and functional molecular machinery.