Neem is considered as a treasured tree species worldwide for its innumerous benefits to the mankind including exclusive therapeutic properties other than its use in medicine, forestry, agriculture and industry. The auspicious attributes of the plant corresponds to its secondary metabolites and the most active constituent is azadirachtin. However, the plant poses limitations to the conventional breeding methods due to its cross pollinating and heterozygous nature resulting into high genetic variability. The heterozygosity in neem causes variations in secondary metabolites production, consequently, it affects the commercial market in the field of medicine and agriculture. These challenges are overcome by the implementation of Plant tissue culture techniques. The technique offers substantial methodologies for genetic improvement, production of homozygous lines and large-scale propagation of neem. The somatic embryogenesis is one of the prominent tool of plant tissue culture technology. The chapter describes the methodology and key factors involved in sequential development of somatic embryogenesis in neem. Ontogenic analysis is rewarding at this level for proper differentiation of the observed structures and their conversion into complete plantlets.