Transdermal drug delivery has been regarded as an alternative to oral delivery and subcutaneous injection for its non-invasiveness, improved patient compliance and avoidance of the first-pass effect. However, needleless transdermal delivery of biomacromolecules remains a challenge. Herein, a transdermal delivery platform is developed to achieve highly efficient non-invasive transdermal delivery of biomacromolecules. In this system, fluorocarbon modified chitosan (FCS) is optimized as an effective yet biocompatible transdermal carrier to assemble with different proteins including immune checkpoint blockade (ICB) antibodies, and antigens such as the spike (S) protein of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The formed FCS-containing nanocomplexes exhibited rather effective transdermal penetration ability via both intercellular and transappendageal routes. Interestingly, non-invasive transdermal delivery of ICB antibodies by FCS induced stronger immune responses to treat mouse melanoma compared to intravenous injection of free antibodies, while presenting reduced systemic toxicity. Moreover, transdermal delivery of SARS-CoV-2 vaccine using FCS-containing nanocomplexes resulted in comparable humoral immunity as well as improved cell immunity and immune memory compared to that achieved with subcutaneous vaccine injection. Thus, FCS-based transdermal delivery systems may provide a compelling opportunity to overcome the skin barrier for efficient transdermal delivery of biomacromolecules, widening the range of therapeutics that can be topically administered.