Miniature vortex generators (MVGs) have the potential to control turbulent boundary layers (TBLs). Analyzing the scaled turbulent structure of MVG TBLs in experiments typically requires indirect methods for accurate friction velocity $$U_\tau$$
U
τ
determination. The established methods for $$U_\tau$$
U
τ
determination need to be verified for non-generic TBLs, such as MVG TBLs, especially at near-wake stations. This study compares the performance of the five most common $$U_\tau$$
U
τ
-determination methods when applied to MVG TBLs. The methods are tuned in terms of their free parameters and fitting ranges using direct measurements of $$U_\tau$$
U
τ
from large eddy simulation data, and applied to a corresponding experiment to assess their accuracy. Based on the findings, an “inner” method, which is the Musker function with a drifting buffer layer incorporating a bump function, is recommended for MVG TBLs of the form investigated, as it provides a good estimation of $$U_\tau$$
U
τ
with uncertainty $$<3\%$$
<
3
%
for all streamwise stations. The method is applied to three further experimental tests with different flow conditions to study trends in $$U_\tau$$
U
τ
. The error of the drag variation is $$<6\%$$
<
6
%
, which indicates the method is reliable for MVG TBLs at high Reynolds numbers.