In this article, molecular dynamics based simulations were carried out to study the effect of Nb in conjunction with grain boundary configurations on the fracture behaviour of bi-crystalline zirconium–niobium alloy (Zr–Nb). A separate set of simulations were performed with a varying percentage of Nb to study its effect on fracture behaviour of Zr–Nb alloy. Simulations were carried out with the crack orientation either perpendicular or parallel to the grain boundary plane. The distance of the crack tip from the grain boundary (GB) plane and percentage of Nb significantly affects the fracture behaviour of alloy. It was concluded from the atomistic simulations that the GB plane in vicinity of the crack tip helps in mitigating the stresses experienced at the tip; whereas the crack tip experienced higher level of stresses when at a distance from the GB plane. Higher angle grain boundaries generate a higher shielding effect at the crack tip as compared to bi-crystals containing lower angle GBs. So far, Zr–Nb alloys are developed with a range of Nb constituent ranging from 0.5% to 5%, results of this article will help in optimising the percentage of Nb in Zr–Nb alloy with desired structural strength.