A culture medium provides the major environmental conditions for cells in vitro. Replenishment of a culture medium causes an abrupt change in the extracellular environment for maintaining cells in a certain state. As a primitive form of a complex system, a stem cell is likely to be influenced by culture conditions that can change the destination of development. To understand how the change in extracellular environment can influence a biological system, we studied the effect of culture media replacement on the gene expression of differentiating neural progenitor cells. From time-series microarray gene expression data of neural progenitor cells, we observed a periodic wave that was synchronized with intermittent culture media replacement. We identified three modes that mostly contribute to the periodic patterns in gene expression and investigated mode-related genes that are sensitive to the changes in the extracellular environment. The biological significance of the three modes was explored, such as progressive development and cell fate decision, extracellular matrix reassembly, and cell growth regulation in response to stress. In addition, we explored systemic influences of media replacement on differentiating neural progenitor cells. Intermittent culture media replacement interrupts expression of genes that participate in the major processes of differentiating neural progenitor cells. This study shows how the abrupt changes in the cell environment influence gene expression systematically.