Friction stir welding (FSW) is a solid state joining process which utilizes the frictional heat of a high speed rotating tool to soften the adjoining sections and stirred/joined them together as one part without filler. In the FSW of pipe joining, a tool rotating at high speeds will start and stop at the same point in order to complete full weld cycle. The FSW of a small diameter pipe can cause secondary heating to occur at the start and stop point. Several pipe samples of 89 mm outside the diameter were prepared based on several specified welding parameters at a stationary position and completed the weld cycle. The Bridgeport 2216 CNC Milling Machine and a customised orbital clamping unit (OCU) were fully utilized for the sample�s preparation. This present study analysed the variation in hardness due to secondary heating for a small pipe diameter. The hardness varies between 18.7 HRB minimum to 33.6 HRB maximum, yielding to lower value due to this condition. © Springer Science+Business Media Singapore 2016.