This paper presents an analytical modeling approach to predict the three-dimensional (3D) dynamics of rotating micro-endmill dynamics considering the attachment errors. Since the fluted section of the cutting tools presents 3D coupled motions such as coupled bending-bending-torsional-axial motions, a 3D solution approach is needed to accurately solve the dynamics of (rotating) micro-tools. Using the presented technique, first, the integral boundary value problem (IBVP) is derived through extended Hamilton’s principle for the circular cross-sectioned sections and fluted sections of the micro-endmill, individually. The numerical solution of the obtained IBVP is solved using a spectral-Tchebychev (ST) technique, where the unknown displacements are expressed as a triple expansion of Tchebychev polynomials. A component mode synthesis (CMS) approach is used to couple the dynamics of each section of the micro-tool. The presented solution technique is applied to predict the dynamics of a rotating micro-endmill. To validate the presented approach, the calculated natural frequencies are compared to those calculated by finite element (FE) solvers. The effectiveness of the model is demonstrated by analyzing (1) the effect of rotational (spindle) speed on the micro-endmill dynamics, (2) the impact of tool attachment errors (tool tilt and eccentricity) on the dynamic response of the micro-endmill tip. It is concluded that the 3D-ST technique can be used for accurate and numerically efficient solution of rotating micro-endmill vibrations.