Developing versatile joining techniques to weld transparent materials on a micrometer scale is of great importance in a growing number of applications, especially for the fabrication and assembly of biomedical devices. In this paper, we report on fs-laser microwelding of two transparent layers of polymethyl methacrylate (PMMA) based on nonlinear absorption and localized heat accumulation at high repetition rates. A fiber CPA laser system was used delivering 650-fs pulses at 1030 nm with repetition rates in the MHz regime. The laser-induced modifications produced by the focused beam into the bulk PMMA were firstly investigated, trying to find a suitable set of process parameters generating continuous and localized melting. Results have been evaluated based on existing heat accumulation models. Then, we have successfully laser welded two 1-mm-thick PMMA layers in a lap-joint configuration. Sealing of the sample was demonstrated through static and dynamic leakage tests. This fs-laser micro-welding process does not need any pre-processing of the samples or any intermediate absorbing layer. Furthermore, it offers several advantages compared to other joining techniques, because it prevents contamination and thermal distortion of the samples, thus being extremely interesting for application in direct laser fabrication of microfluidic devices.