Background Goats undergoing road transportation are subjected to inverse organismal disturbances in the external environment, with high temperatures, bumps, and complex microbial environments during transportation linking to compound stressors, which can trigger pathological apoptosis and autophagy. Pathological cell death dysregulating the homeostasis of the internal environment of the organism and thus causing immunosuppression and tissue damage. Bcl-2 and Bax are a pair of functional antagonistic proteins regulating apoptosis, p62, LC3B and the PINK1/Parkin pathway have also been shown to play important mediating roles in the process of cellular autophagy. The aim of this study was to investigate the effects of transportation stress on proteins related to apoptosis and autophagy in goat lung cells. Nine healthy male Ganxi goats were selected and divided into control group without transport (0h transport group), 2h transport group, 6h transport group, three in each group, and the lungs were taken after treatment. Results The results of the study showed that transportation stress increased the apoptosis rate in goat lungs, which was significantly higher in the 2h transportation group than in the 6h transportation group and the control group. Apoptotic proteins Bcl-2 and Bax were mainly expressed in the bronchial epithelium at all levels as well as in the alveolar septum. Autophagy-associated LC3B proteins were distributed in the cytoplasm of alveoli and bronchioles, and p62, PINK1 and Parkin proteins were widely expressed in the alveolar epithelium and the cytoplasm of cells in specific sites and nuclei. Also, there was a significant downregulation of PINK1 and Parkin proteins after the 6h transportation. Apoptosis-associated Bcl-2 and Bax genes and autophagy-associated LC3B, p62, PINK1 and Parkin genes showed different degrees of dysregulation after a certain time of transport, respectively. Conclusion The results of our study indicate that transportation stress could lead to an up-regulation of apoptosis rate in goat lung cells, which exhibited both a significant effect on the expression levels of apoptosis-related Bcl-2 and Bax genes, and triggered a dysregulation of autophagy-related LC3B, p62, PINK1 and Parkin genes, suggesting that transportation stress is closely related to apoptosis and autophagy in the lungs of goats.