Most massive stars reside in binary or multi-object systems. Short gamma-ray bursts (sGRBs), the product of the merger of double compact objects, may originate from massive common-envelope binaries. In contrast, the progenitors of long GRBs (lGRBs) are typically considered isolated massive stars. However, no effective method has yet been established to identify potential companions from current observations. Recent studies have demonstrated that quasi-periodic oscillation signatures can serve as a promising tool to probe the properties of GRB central engines. In this study, by drawing an analogy to periodicity in X-ray binaries, we explore the precession periods of companion-induced disk precession for lGRBs born in the ultra-compact binary scenario. Our results suggest that the periodicity observed in lGRB afterglows, measured in units of 1000 s or more, may indicate that lGRBs originate within binary systems. GRB 050904 could represent a rare case where the burst occurred in a binary system, leaving behind a black hole–black hole binary at redshift z = 6.29.