Numerical simulation has been conducted for the chaotic flow in a 3D closed-loop pulsating heat pipe (PHP). Heat flux and constant temperature boundary conditions were applied for evaporator and condenser sections, respectively. Water and ethanol were used as working fluids. Volume of fluid (VOF) method has been employed for two-phase flow simulation. Spectral analysis of temperature time series was carried out using power spectrum density (PSD) method. Existence of dominant peak in PSD diagram indicated periodic or quasi-periodic behavior in temperature oscillations at particular frequencies. Correlation dimension values for ethanol as working fluid were found to be higher than that for water under the same operating conditions. Similar range of Lyapunov exponent values for the PHP with water and ethanol as working fluids indicated strong dependency of Lyapunov exponent on the structure and dimensions of the PHP. An O-ring structure pattern was obtained for reconstructed 3D attractor at periodic or quasi-periodic behavior of temperature oscillations. Minimum thermal resistance of 0.85 °C/W and 0.88 °C/W were obtained for PHP with water and ethanol, respectively. Simulation results showed good agreement with the experimental results from other work under the same operating conditions.