Niobium based Nb-1Zr-0.1C alloy has been developed for high temperature applications. Welding ofthis alloy is difficult task due to its reactive nature, higher thermal conductivity and melting point. In thepresent work, Electron Beam (EB) welding technique, which can produce narrow deep penetration weldswith nominal heat affected zone (HAZ) and minimum contamination, is used to weld the alloy. This workis aimed to produce the acceptable EB welds of Nb-1Zr-0.1C alloy. For this purpose, EB welds of Nb-alloy inbead-on-plate and square butt joint configurations were produced according to central composite designof the experiments with power (P) and weld speed (S) as input process parameters. The output of thewelding process was measured in terms of depth of weld penetration (D), weld bead width (W), aspectratio, joining efficiency and thermal efficiency. The correlations for D and W, as a function of processparameters, were obtained by non-linear statistical regression analysis. The weld joints produced werecharacterized by optical, Scanning Electron Microscopy (SEM) and Electron Back Scattering Diffraction(EBSD) techniques. The HAZ and base metal showed fine carbide precipitates along the grain boundaries,whereas carbides were found dissolved in the weld zone. The micro-hardness profile across the width ofwelds showed marginal increase in the hardness of weld zone and HAZ. Thermal and residual stress fieldswere estimated for the EB weld joint in square-butt configuration, using finite element technique and agood qualitative matching between the computed and experimental values was obtained. The detailedresults of all these studies are described in this paper.