代谢工程学是指利用基因工程或是分子生物学技术，将生体内之代谢途径改变，通常改变生体内化学反应之酶。它来自于发酵学。代谢工程技术目前以微生物利用为主，改变工业微生物之代谢路径，生产所需要的化学物质，如抗生素。

代谢工程（Metabolic engineering）又称途径工程，一般定义为通过某些特定生化反应的修饰来定向改善细胞的特性，或是利用重组DNA技术来创造新的化合物。

这一概念由美国学者Bailey J E于1991年首先提出。其将代谢工程定义为：用重组DNA技术来操纵细胞的酶运输和调节功能从而改进细胞的活性。Stephanopouls等认为，代谢工程是一种提高菌体生物量或代谢物产量的理性化方法。Cameron等的定义则精炼一些，即用重组DNA技术有目的地改造中间代谢。

Metabolic engineering is the practice of optimizing genetic and regulatory processes within cells to increase the cells' production of a certain substance. These processes are chemical networks that use a series of biochemical reactions and enzymes that allow cells to convert raw materials into molecules necessary for the cell’s survival. Metabolic engineering specifically seeks to mathematically model these networks, calculate a yield of useful products, and pin point parts of the network that constrain the production of these products. Genetic engineering techniques can then be used to modify the network in order to relieve these constraints. Once again this modified network can be modeled to calculate the new product yield.