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An inventory system is considered for continuous decaying items with non-zero lead time and stochastic demand when shortages are allowed and all unsatisfied demands are backlogged. In this research we consider orders as separate packages where replenishment is one-for-one and a modified base stock policy is applied. In this paper, a penalty cost is introduced for stochastic inventory models with decaying items when less than one unit of the product is delivered to the customers. The objective of the warehouse is to maximize his average profit. Since the concavity analysis of the model is extremely complicated, an upper bound is introduced and an algorithm is presented for finding the optimal solution. Finally, a numerical example is presented and sensitivity analysis is carried out for a number of important parameters.