Abstract: Two types of embedded microball lenses namely convex microball lens ( VMBL) and concave microball lens ( CMBL ) with outstanding optical properties were successfully fabricated inside a polymethethyl methacrylate ( PMMA) substrate by utilizing a high repetition rate femtosecond fiber laser. The fabricating mechanism of the VMBL was refractive index change induced by femtosecond laser, and the CMBL was fabricated due to the multiphoton absorption and the heat accumulation effect of the successive laser pulses irradiation at a high repetition rate. As an example, the CMBL fabrication efficiency with 20 × and 50 × microscopic objectives was compared. The principles for choosing a proper objective when fabricating customized embedded lens were also discussed. Additionally, these lenses can be used as powerful tools in constructing specific micro-optic systems towards various applications. This technology also allows the direct fabrication of microlens inside microfluidic devices to enhance the ability of gathering fluorescence signals and optical imaging. It is very possible to fabricate a function-integrated microfluidic chip in one-step by utilizing this technology in the near future.