BODIPY and BODIPY‐derived systems are widely applied as fluorophores and as probes for viscosity detection in solvents and biological media. Their orientational and rotational dynamics in biological media are thus of vital mechanistic importance and extensively investigated. In this contribution, polarization‐resolved confocal microscopy is used to determine the orientation of an amphiphilic BODIPY‐cholesterol derivative in homogeneous giant unilamellar vesicles (GUV) made from 1,2‐dioleoyl‐sn‐glycero‐3‐phosphocholine (DOPC). The BODIPY‐moiety of the molecule is placed near the polar headgroups, and the cholesterol moiety is embedded in the membrane along the acyl chain of the lipids. The rotational relaxation of fluorophore is conventionally investigated by time‐resolved emission anisotropy (TEA); and this method is also used here. However, TEA depends on the emission of the fluorophore and may not be useful to probe rotational dynamics of the non‐emissive triplet states. Thus, we employ femtosecond transient absorption anisotropy (TAA), that relies on the absorption of the molecule to complement the studies of the amphiphilic BODIPY in DCM and GUV. The photoinduced anisotropy of the BODIPY molecule in DCM decays tri‐exponentially, the decay components (sub‐5 ps, 43 ps and 440 ps) of anisotropy are associated with the non‐spherical shape of the BODIPY molecule. However, the anisotropy decay in homogenous GUVs follows a biexponential decay; which arises from the wobbling‐in‐a‐cone motion of the non‐spherical molecule in the high viscous lipid bilayer media. The observations for the BODIPY‐chol molecule in the GUV environment by TAA will extend to the investigation of non‐emissive molecules in cellular environment since GUV structure and size resembles the membrane of a biological cell.