The phytohormone ethylene can cause adverse effects in plants, including inhibition of shoot elongation and abscission of leaves, flowers and fruits. 1-Methylcyclopropene (1-MCP) is a competitive inhibitor of ethylene binding with the ethylene receptors and prevents ethylene responses. To determine the effectiveness of 1-MCP as an ethylene prophylactic for cotton, an assay system was developed that integrated analyses of leaf declination, shoot elongation and ethylene-responsive gene expression (GhACS6, GhACO5, GhEIN4, GhLTL1). Using a flow-through controlled growth system, the optimal parameters of ethylene treatment in eliciting responses and of 1-MCP treatment in preventing these responses, were determined. Shoot elongation and gene expression changes in response to ethylene correlated well, but gene expression changes were found to offer a more robust estimate of ethylene responsiveness. The effect of ethylene treatment on the expression of the marker genes was determined to be optimal with 3 h of 10 μL L−1 fumigation. 250 nL L−1 of gaseous 1-MCP provided for 1 h immediately before ethylene fumigation was highly efficacious at preventing ethylene responses, but the duration of protection did not exceed 48 h. A liquid formulation of 1-MCP designed for field use was found to be equally effective as the gas. The results, and the system described, may prove useful in increasing 1-MCP efficacy as a tool to manage the negative effects of stress ethylene in cotton crops.