The aim of this study is to design and evaluate a transdermal delivery system for alendronate sodium (ALS) loaded with nanocarrier to improve its permeability and prolong its release. This is due to its low bioavailability, potential gastrointestinal side effects, and the special administration needed for the oral dosage form of ALS. When using the ether injection method, various niosomal formulations were produced. Size of the particles, polydispersity index (PDI), surface charge (ZP), drug entrapment efficiency (EE), and in vitro release were used to characterize the resulting niosomes. The size of niosomes ranged between 99.6 ± 0.9 and 464.3 ± 67.6 nm, and ZP was from −27.6 to −42.27 mV. The niosomal formulation was then loaded to aqueous polymer solution of 30% polyvinyl pyrrolidone (PVP) (MN-1), 30% PVP with 15% poly(vinyl alcohol) (PVA) (2:1) (MN-2), and 30% PVP with 15% PVA (1:1) (MN-3). The cumulative amount of ALS (Q) was in the following order: MN-1 > MN-2 > MN-3. All formulations in this study were stable at room temperature over two months, in terms of moisture content and drug content. In conclusion, a transdermal delivery of ALS niosomes combined in microneedles (MNs) was successfully prepared to provide sustained release of ALS.