In this article a medicinal oil (neem oil) is fractionated and compared with original oil. The fractions were separated at low temperature using chloroform and methanol. The uniphase mixture of solvents and neem oil at room temperature was transformed to a bi-phasic system at low temperature. The isolated fractions (NOC – isolated using chloroform; NOM – isolated using methanol) were characterized and differentiated by GC, FT-IR and Rheometer. GC and FTIR have well revealed the difference in composition of fatty acids in fractions – NOC; NOM and neem oil (NO). Rheologically all the oils are different in viscosity from parent oil. The NOM fraction of neem oil showed newtonian behavior while NOC shows a non-newtonian behavior. It can be concluded from data that fractions NOC, NOM can be used for targeting drugs using various formulation approaches.