Malaria elimination programmes are dependent on a rapid, cost‐effective and portable diagnostic tool to detect and quantify malaria parasites in human blood. Herein, we report a cost‐effective and portable nuclear magnetic resonance (pNMR) for malaria diagnosis. In this present study, we have developed and characterized a sensitive and low‐cost novel on‐chip NMR probe. This NMR probe has improved mismatching problem between radiofrequency (RF) coil and transmission line that results in enhancement in NMR sensitivity. Developed pNMR represents a rapid, cost‐effective and highly sensitive method to detect very low parasitaemia plasmodium falciparum (0.0001%) in infected human blood in comparison with other available malaria diagnosis techniques. The experimental results show that very low parasitic load can be detected rapidly by the change in the transverse relaxation rate (T2) of NMR, suggesting a good sensitivity. A good linear relationship with a correlation coefficient of 0.94 between the change in transverse relaxation rate (ΔT2) and the different parasitaemia (%) has been observed, indicating that pNMR is a potential tool for real‐time, reusable and high‐sensitivity analysis of malaria parasite in human blood.