Steroid hormone 20-hydroxyecdysone and the sesquiterpenoid juvenile hormone are the main regulators of insect development; however, it is unclear how they interact in the regulation of metamorphic events. Using the silkworm, Bombyx mori, we show that the juvenile hormone analogue fenoxycarb affects the cascade of ecdysone regulated genes that control the programmed cell death in the larval midgut. Morphological changes that occur during cell death were investigated by studying cross-sections of the midgut stained with hematoxylin and eosin. Apoptosis-specific DNA fragmentation was detected using TUNEL assay. Expression patterns of genes ATG8 and ATG12, which were used as indicators of autophagy, and genes of the ecdysone-regulated gene cascade were examined using real-time quantitative polymerase chain reaction. Fenoxycarb application on day 0 of the 5th larval instar extended the feeding period and postponed programmed cell death in mature larval midgut. This effect was probably due to a delay in ecdysone secretion and associated changes in gene expression were mostly not a direct response to the fenoxycarb. However, differences in the gene expression patterns in the control and fenoxycarb treated insects during the prepupal and early pupal stages indicated that fenoxycarb may also exert a more direct effect on some genes of the ecdysone regulated gene cascade.