Electroencephalography (EEG) monitoring is known to be technically feasible and possibly clinically relevant to determine patients with acute ischaemic hemispheric stroke. The EEG is a very useful tool in understanding neurological dysfunction of stroke and likely improving the treatment and rehabilitation. The traditional method for diagnosing with EEG is mainly based on conventional Fast Fourier Transform (FFT). FFT is known to be limited to linear and stationary signal processing. Previously, a technique known as Brain Symmetry Index (BSI) has been proposed to determine the index value for asymmetry of blood flow in right and left brain hemispheres. The estimated index between stroke patient and healthy person ranges between zero and one. Similarly, the existing standard BSI limit the frequency band until 25Hz to eliminate EMG artifact, but at higher frequency band some useful information can also be represented. Hence, highlighting the limitation of FFT in providing the coefficient to calculate BSI index. In this study, we employed the Hilbert Huang Transform (HHT) to extract important feature for this research to use as coefficient in calculating the BSI index for stroke patients with multifocal infarction and healthy individuals. The proposed BSI-HHT spectral analysis conducted in this research was compared with several existing BSI techniques. In order to validate the performance of BSI-HHT, we conducted two experiments 1) 1-25Hz and 2) 1-64Hz for both patients and healthy individuals. The proposed technique offers constant BSI index for two cases and providing better resolution results in determining the index as compared to the existing BSI techniques.