We investigated the effect of cross-sectional shape and size on the light-extraction efficiency (LEE) of GaN-based blue nanorod light-emitting diode (LED) structures using numerical simulations based on finite-difference time-domain methods. For accurate determination, the LEE and far-field pattern (FFP) were evaluated by averaging them over emission spectra, polarization, and source positions inside the nanorod. The LEE decreased as rod size increased, owing to the nanorods’ increased ratio of cross-sectional area to sidewall area. We compared circular, square, triangular, and hexagonal cross-sectional shapes in this study. To date, nanorod LEDs with circular cross sections have been mainly demonstrated experimentally. However, circular shapes were found to show the lowest LEE, which is attributed to the coupling with whispering-gallery modes. For the total emission of the nanorod, the triangular cross section exhibited the highest LEE. When the angular dependence of the LEE was calculated using the FFP simulation results, the triangular and hexagonal shapes showed relatively high LEEs for direction emission. The simulation results presented in this study are expected to be useful in designing high-efficiency nanorod LED structures with optimum nanorod shape and dimensions.