Methane emissions from enteric fermentation in dairy cows make a substantial contribution to the greenhouse gas problem. Sniffer approaches represent a popular low-cost, mobile technology for cow gas emission measurement in industrial installations owing to their providing reliable emission estimates. Despite its advantages, the sniffer approach often yields data inconsistencies during automated acquisition due to unsynchronized clocks between sniffers and associated automatic milking machines, leading to uncertainty in the linking of each animal's data with methane emission records. Given the constantly growing demand for large-scale methane emission measurements for genetic studies, sniffer installations are expected to increase, making the need for an efficient solution to the data synchronization issue prescient. A novel approach for handling the synchronization problem was developed in this study based on matched filter theory. The approach was verified on gas emission data from multiple commercial dairy farms in Denmark. The results were analyzed and discussed in terms of accuracy and general characteristics of computational performance irrespective of a specific software implementation. The present findings support the conclusion that the presented matched filter-based approach is robust, applicable to the problem of cattle gas emission data synchronization, and convenient for automated data processing.