The recent developments in the production of miniaturized devices increases the demand on micro-components where the thickness ranges from tens to hundreds of microns. Various challenges, such as size effect and stress concentrations at the grain boundaries, arise due to the deformation heterogeneity observed at grain scale. Various metallic alloys, e.g. aluminum, exhibit substantial localization and stress concentration at the grain boundaries. In this regard, inter-granular damage evolution, crack initiation and propagation becomes an important failure mechanism at this length scale. Crystal plasticity approach captures intrinsically the heterogeneity developing due to grain orientation mismatch. However, the commonly used local versions do not possess a specific GB model and leads to jumps at the boundaries. Therefore, a more physical treatment of grain boundaries is needed. For this purpose, in this work, the Gurtin GB model (Gurtin (2008)) is incorporated into a strain gradient crystal plasticity framework (Yalcinkaya et al. (2011), Yalçinkaya et al. (2012), Yalçinkaya (2017)), where the intensity of the localization and stress concentration could be modelled considering the effect of grain boundary orientation, the mismatch and the strength of the GB. A zero thickness 12-node interface element for the integration of the grain boundary contribution and a 10-node coupled finite element for the bulk response are developed and implemented in Abaqus software as user element subroutines. 3D grain microstructure is created through Voronoi tessellation and the interface elements are automatically inserted between grains. After obtaining the localization, the mechanical behavior of the GB is modelled through incorporation of a potential based cohesive zone model (see Park et al. (2009), Cerrone et al. (2014)). The numerical examples present the performance of the developed tool for the intrinsic localization, crack initiation and propagation in micron-sized specimens.