In this work, the authors present the computational fluid dynamics (CFD) studies carried out to understand the influence of contact angle on the bubble transport in a rectangular bifurcating microchannel. The bifurcating microchannel mimics a human arteriole. Blood is modeled as Newtonian fluid and a single occluding perfluorocarbon (PFC) bubble is transported through the microchannel. The static contact angles are given as an input via. the in-built module in the commercial CFD package, ANSYS® and the dynamic contact angles via. an user defined function (UDF). It was found that for each of the contact angles, the bubble meniscus shape is different. The distribution of the bubble volume in the daughter channels is dependent on this meniscus shape and the pulsatile pressure imposed at the inlet. The effect of gravity was also considered to understand its influence on the bubble splitting in the daughter channels. These results will be useful when considering the transport of microbubble contrast agents or encapsulated microbubbles (containing drugs) for the purpose of drug delivery. © Springer International Publishing Switzerland 2014.