An elastic film with water repellency is of great interest for application to waterproof and antifouling surface treatment of stretchable devices such as wearable electronics or functional textiles. Herein, a nanoscale ultrathin stretchable polymer film endowed with superhydrophobicity was newly designed and synthesized by a vapor phase method, initiated chemical vapor deposition (iCVD). The highly stretchable superhydrophobic polymer film was generated from the copolymerization of 1H,1H,2H,2H-perfluorooctyl acrylate (PFOA) and 1,3,5-trivinyl-1,3,5-trimethylcyclotrisiloxane (V3D3) to form a cross-linked fluoropolymer network with low crystallinity and elasticity as well as superhydrophobicity. The composition of the copolymer film was adjusted by controlling the flow rates of the input monomers of PFOA and V3D3 during the deposition process. The copolymer film with the optimized composition showed an elastic limit higher than 200% while maintaining the superhydrophobic property with a water contact angle greater than 150 degrees on nonflat substrates. An 800-nm-thick copolymer thin film showed mechanical durability with superhydrophobic performance even after 2000 cycles of a 200% stretch test. The elastic copolymer film also displayed solvent resistance against incubation in various organic solvents for 24 h. Transparency greater than 90% was also confirmed in the whole visible range with large-area uniformity and conformal coverage. We believe the stretchable superhydrophobic polymer film developed in this study is a promising candidate material for passivation of various stretchable device applications.