Chemical modification of proteins provides powerful tools for creating a broad range of engineered proteins and for elucidating the function and dynamics of proteins in multimolecular crowding systems, such as those in live cells and living organisms. Over the past two decades, a number of strategies for conjugating desired probes or artificial functionalities to target proteins have been developed. However, the chemical modification of native proteins in a site-specific and target-selective manner under complex biological conditions still remains challenging, because the applicable chemical reactions needed to achieve such modifications are currently very limited. Despite this, a variety of bioorthogonal strategies have recently emerged to address this crucial issue. In this chapter, we introduce recently developed bioorthogonal click chemistries and methods for incorporating click handles into proteins, which can potentially be employed for the chemical modification of proteins in biological systems. Additionally, recent examples for click chemistry-based protein labeling in live cells and animals are briefly described.