In principle, the Hamiltonian represents the energy of a system. Whether or not you want to model your system to have kinetic energy is up to you and what you need. For example: consider an atom with an electron that can be approximated as a two level system (i.e. it as only its ground state and an excited state).
The ground state $|g\rangle$ has some energy $E_0$, and the excited state $|e\rangle$ has some energy $E_0+\Delta E$, you are always free to chose the ground state energy as you like, so chose $E_0=-\frac{\Delta E}{2}$ and you have the Hamiltonian of your system
$$H=\frac{\Delta E}{2}\left(|e\rangle\langle e|-|g\rangle\langle g|\right)=\frac{\Delta E}{2}\begin{pmatrix}-1&0\\0&1\end{pmatrix}=-\frac{\Delta E}{2}\sigma_z $$
with $\sigma_z$ the Pauli matrix. This is a perfectly valid (albeit a bit boring) Hamiltonian that has no kinetic term, basically, you decided that you don't really care about the kinetic energy of the atom, you're interested in the state of the electron. More interesting Hamiltonians that don't model kinetic degrees of freedom are given in Paradoxy's answer.
And as a note, a Hamiltonian is just a hermitian operator bounded below. There is, in principle, no further requirement. You can take any hermitian operator bounded below and start solving the Schrödinger equation. Of course, whether or not this has any physical meaning is another story.