In this study, the applicability of hydride generation atomic fluorescence spectrometry (HG-AFS) and inductively coupled plasma mass spectrometry (ICP-MS), methods I and III specified in the national standard GB 5009.93—2017, respectively to detect selenium in infant formula for special medical purposes was researched. Seven laboratories separately determined the selenium content in six samples of 3 types of infant formula for special medical purposes and infant formula quality control samples, and measured the recoveries. The results showed both methods were suitable for the determination of selenium in infant formula, while the applicability for various types of infant formula foods for special medical purposes needs to be further studied.