In this study, we report the bioorthogonal cleavage of physiologically stable methylene tetrazines bearing an ether or ester linkage in the presence of trans-cyclooctene. Based on this approach, molecules with phenol or carboxylic acid moieties were efficiently released in a controlled manner, which can be effectively applied in living cells. We expect this bioorthogonal cleavage approach can be applied to several biomedical applications, including the development of antibody-drug conjugates, pretargeted prodrug release, and protein activation.