A highly efficient and general protocol for traceless, directed C3-selective C–H borylation of indoles with [Ni(IMes)2] as the catalyst is reported. Activation and borylation of N–H bonds by [Ni(IMes)2] is essential to install a Bpin moiety at the N-position as a traceless directing group, which enables the C3-selective borylation of C–H bonds. The N-Bpin group which is formed is easily converted in situ back to an N–H group by the oxidative addition product of [Ni(IMes)2] and in situ-generated HBpin. The catalytic reactions are operationally simple, allowing borylation of a variety of substituted indoles with B2pin2 in excellent yields and with high selectivity. The C–H borylation can be followed by Suzuki–Miyaura cross-coupling of the C-borylated indoles in an overall two-step, one-pot process providing an efficient method for synthesizing C3-functionalized heteroarenes.