This study details the development of an effective synthetic method and proposes a reaction mechanism for the preparation of fused thieno[3,2-d][1,3]oxazine from the corresponding amino acid. Investigation into the nature of primary amine properties on reactions with condensed thieno[3,2-d]oxazine revealed their role in forming either fused thieno[3,2-e]pyridines or thieno[3,2-d]pyrimidines. Furthermore, synthesis reaction mechanisms for both tri- and tetracyclic systems were provided. Notably, regioselective alkylation of condensed thieno[3,2-d]pyrimidin-(3H)-one led to the synthesis novel N-alkyl derivatives.