In this research, we aim to quantify the difficulty of program comprehension during source code reading. We use Near Infra-Red Spectroscopy(NIRS) to measure the activation of brain. As a result of an experiment with 10 subjects, 8 of them showed a strong activation in the brain during reading of strongly obfuscated programs that are extremely difficult to comprehend. We also normalized the data for each participant and aggregated them for statistical testing. As a result of t-test, significant difference (p < 0.001) was seen in the mean of the brain blood flow between obfuscated and non-obfuscated programs.