I have gene expression profile of human in FPKM scale, when I take look into expression distribution, the mean is close to zero. Does it make sense ? the FPKM value for most of the genes are small and it's close to zero.
When I create box plot of expressed genes, the median is very close to zero. Is it normal or something might going wrong with my data?
I agree. To emphasis this point, think that in a total RNA extract, you'll have about 95% rRNA (only a few genes !), the remaining 5% being split mostly between tRNAs and mRNAs.
Log transformation of your data (you might need pseudocounts) before the boxplot is a good idea.