The congruence subgroup problem for a finitely generated group Γ and for G ≤ Aut ( Γ ) G\leq\mathrm{Aut}(\Gamma) asks whether the map G ^ → Aut ( Γ ^ ) \hat{G}\to\mathrm{Aut}(\hat{\Gamma}) is injective, or more generally, what its kernel C ( G , Γ ) C(G,\Gamma) is. Here X ^ \hat{X} denotes the profinite completion of 𝑋. In the case G = Aut ( Γ ) G=\mathrm{Aut}(\Gamma) , we write C ( Γ ) = C ( Aut ( Γ ) , Γ ) C(\Gamma)=C(\mathrm{Aut}(\Gamma),\Gamma) . Let Γ be a finitely generated group, Γ ¯ = Γ / [ Γ , Γ ] \bar{\Gamma}=\Gamma/[\Gamma,\Gamma] , and Γ * = Γ ¯ / tor ( Γ ¯ ) ≅ Z ( d ) \Gamma^{*}=\bar{\Gamma}/\mathrm{tor}(\bar{\Gamma})\cong\mathbb{Z}^{(d)} . Define Aut * ( Γ ) = Im ( Aut ( Γ ) → Aut ( Γ * ) ) ≤ GL d ( Z ) . \mathrm{Aut}^{*}(\Gamma)=\operatorname{Im}(\mathrm{Aut}(\Gamma)\to\mathrm{Aut}(\Gamma^{*}))\leq\mathrm{GL}_{d}(\mathbb{Z}). In this paper we show that, when Γ is nilpotent, there is a canonical isomorphism C ( Γ ) ≃ C ( Aut * ( Γ ) , Γ * ) . C(\Gamma)\simeq C(\mathrm{Aut}^{*}(\Gamma),\Gamma^{*}). In other words, C ( Γ ) C(\Gamma) is completely determined by the solution to the classical congruence subgroup problem for the arithmetic group Aut * ( Γ ) \mathrm{Aut}^{*}(\Gamma) . In particular, in the case where Γ = Ψ n , c \Gamma=\Psi_{n,c} is a finitely generated free nilpotent group of class 𝑐 on 𝑛 elements, we get that C ( Ψ n , c ) = C ( Z ( n ) ) = { e } C(\Psi_{n,c})=C(\mathbb{Z}^{(n)})=\{e\} whenever n ≥ 3 n\geq 3 , and C ( Ψ 2 , c ) = C ( Z ( 2 ) ) = F ^ ω C(\Psi_{2,c})=C(\mathbb{Z}^{(2)})=\hat{F}_{\omega} is the free profinite group on countable number of generators.