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We derive the Hamiltonian function for extended teleparallel theories of gravity in their covariant formulation. In particular, we present the Hamiltonian for $f(T)$ gravity and New General Relativity. From this, we obtain the related Hamilton equations, which are presented both in covariant formulation and Weitzenb\"ock gauge. In this framework, teleparallel equivalent to General Relativity, its $f(T)$ extension and New General Relativity can be compared. We find that $f(T)$ and New General Relativity consistently reduce to the Teleparallel Equivalent to General Relativity, while significant differences appear comparing the Hamilton equations of $f(T)$ with $f(R)$ gravity.