Pulsating heat pipe (PHP) is an implicit technique through a passive two-stage heat transfer system. This paper presents the experimentations on PHP contrived using copper with different inner tube diameters of 1, 1.5, 2, and 2.5 mm, respectively. The PHP is accused of acetone as a functional liquid with filling proportions varying from 50 to 90% of its volume with an increment of 10%. The effects of filling proportion and tube diameter on the thermal performance of PHP were investigated. The evaporator zone is electrically heated using a mica heater in the range of 20–80 W, and the condenser area is kept cool by the water circulation method. The results show that a 2 mm inner tube diameter performs best compared to other tube diameters, with a lower rate of thermal resistance of 0.49 K/W. Also, the performance of PHP is enhanced at a filling proportion of 60% for all the tube diameters. Further, CFD analysis was carried out for different filling ratios for a 2 mm diameter pipe at a constant heat input of 80 W, and it revealed that test outcomes were in line with CFD results. The deviation between the experimental and numerical studies was 10%. Considering the optimized parameters, i.e., tube diameter and filling ratio, the work was extended by adding SiO2 nanoparticles to the base fluid with 1–5 % mass concentration. The results showed a lower thermal resistance value of 0.3 W/K and a higher heat transfer coefficient of 828.64 W/m2 °K was obtained at 2% mass concentration of SiO2. Also, the proportional rise in heat transfer coefficient at 60 W is 11.46, 17, 14, 4.15, and 1.94% for 1, 2, 3, 4, and 5% mass concentration of SiO2 nanoparticles, respectively. Hence, the PHP operates better at a 2 mm diameter with a 60% filling ratio and 2% mass concentration of SiO2 nanoparticles.