From the literature it is found that, two different approaches were followed for the prediction of transverse thermal conductivity (K2) of FRP composites. In the first approach, the internal anisotropy of the lamina is assumed negligible and K2 is estimated using simple Fourier's law of 1-D heat conduction applied to Representative Volume Element (RVE). Whereas in the second approach, electrical analogy method is followed. To estimate the effect of internal anisotropy, through thickness thermal conductivity (K3) of an FRP lamina is determined by both the approaches using the Finite Element method for an RVE in the auxiliary plane. The problem is modelled in ANSYS 15 software. In the present paper studies are made for various Kf/Km values (1-50) and for various angles (200-900) made by the section plane with the fiber axis. It is observed that the through thickness thermal conductivity is consistent in the second approach, whereas in the first approach there is considerable variation (max. 8.6%) with the orientation of the unit cell.