Carbon nanofibers (CNFs) have been used for applications in composite material for decades because of their unique mechanical, thermal, and electrical properties. Consequently, an in-depth understanding of mechanical properties of individual CNFs, particularly after chemical functionalization, would provide important insight into its effective integration into composite materials. Fluorination and amination of CNFs is achieved and systematic chemical characterizations of functionalized CNFs are performed. An in situ tensile testing method, which combines a simple microfabricated device with a quantitative nanoindenter inside a scanning electron microscope (SEM) chamber, is used to measure mechanical properties of individual pristine, fluorinated, and amino-functionalized CNFs. The nominal CNFs strengths follow the Weibull distribution and the fluorinated CNFs are found to possess higher nominal strength but similar strain when compared with the pristine and amino-functionalized CNFs. SEM fracture surfaces analysis shows that all nanofibers failed in a similar cup-and-cone fashion. Microscopy image sof fluorinated CNFs reveal an unexpected change in the hollow core before and after fiber fracture, which is attributed to the possible effects of fluorination-induced compression on nanofiber surfaces. The results demonstrate the potential of fluorination for improving both the mechanical properties of CNFs and their successful integration into composites.