Although many molecular dynamics simulations have been conducted on slip flow on graphene, experimental efforts remain very limited and our understanding of the flow friction on graphene remains far from sufficient. Here, to accurately measure the slip length in rectangular nanochannels, we develop a 3D capillary flow model that fully considers the nonuniform cross-section velocity profile, slip boundary conditions, and the dynamic contact angle. We show that the 3D analysis is necessary even for a channel with a width/height ratio of 100. We fabricated graphene nanochannels with 45-nm depth and 5-μm width, and measured slip lengths of about 30–40 nm using this 3D flow model. We also reevaluated the slip-length data for graphene obtained from capillary filling experiments in the literature: 30 nm instead of originally claimed 45 nm for a 25-nm-deep channel, and 47 nm instead of 60 nm for an 8.5-nm-deep channel. We discover a smaller slip length than existing experimental measurements due to our full 3D flow analysis considered in our method. This work presents a rigorous analysis approach while also providing a better understanding of slip flow in graphene nanochannels, which will benefit further innovation in nanofluidic applications, including electronics cooling and biomedical chips.