Consider an arbitrary quantum system whose state evolves under the Schrödinger equation
$$
i\frac{d}{dt}|\psi\rangle=\hat H|\psi\rangle.\tag{1}\label{eq1}
$$
Let $\hat{\mathbf X}\triangleq\lbrace\hat X_1,\dots, \hat X_n \rbrace$ be any complete set of compatible observables. Let $\lbrace\mathbf x\rbrace$ be the corresponding spectrum and $\lbrace|\mathbf x\rangle\rbrace$ be the corresponding basis of eigenstates. In general, we can define the following probability density and current over the quantum numbers $\mathbf x$ [1]:
\begin{align}
\rho(\mathbf x,t)&\triangleq |\langle\mathbf x|\psi(t)\rangle|^2,\tag{2a}\label{eq2a}\\
j(\mathbf x,\mathbf x',t)&\triangleq 2\Im\left\lbrace\langle\psi(t)|\mathbf x\rangle\langle \mathbf x|\hat H|\mathbf x'\rangle\langle\mathbf x'|\psi(t)\rangle\right\rbrace.\tag{2b}\label{eq2b}
\end{align}
These can be shown to satisfy the following continuity equation as a consequence of eq. \eqref{eq1}:
$$
\frac{\partial\rho(\mathbf x,t)}{\partial t}=\int d^n\mathbf x'\,j(\mathbf x, \mathbf x', t).\tag{3}\label{eq3}
$$
The interpretation is that $\rho(\mathbf x,t)$ is the probability that the outcome $\mathbf x$ is obtained if a measurement of $\hat{\mathbf X}$ is performed at time $t$, while $j(\mathbf x, \mathbf x', t)=-j(\mathbf x', \mathbf x, t)$ is the rate at which that probability flows from $\mathbf x'$ to $\mathbf x$ if the system is left to evolve.
OP's question involves the special case in which the Hamiltonian is of the form
$$
\hat H=\frac{1}{2}\hat{\mathbf P}\cdot\hat{\mathbf P}+V(\hat{\mathbf X}),\tag{4}\label{eq4}
$$
where $\hat{\mathbf P}\triangleq\lbrace \hat P_1,\dots,\hat P_n\rbrace$, is the conjugate of $\hat{\mathbf X}$ (i.e. $[\hat P_i,\hat P_j]=0, [\hat X_i,\hat P_j]=i\delta_{ij}$). In this special case the integral in \eqref{eq3} reduces to
$$
\int d^n\mathbf x'\,j(\mathbf x, \mathbf x', t)=-\frac{\partial}{\partial \mathbf x}\cdot\Im\left\lbrace\psi(\mathbf x,t)^*\frac{\partial}{\partial \mathbf x}\psi(\mathbf x,t)\right\rbrace,\tag{5}\label{eq5}
$$
where $\psi(\mathbf x,t)\triangleq\langle\mathbf x|\psi(t)\rangle$. In this case the continuity equation reduces to the local form that OP seems to be expecting:
$$
\frac{\partial\rho}{\partial t}+\frac{\partial}{\partial\mathbf x}\cdot\mathbf j=0,\tag{6}\label{eq6}
$$
where
$$
\mathbf j(\mathbf x,t)\triangleq \Im\left\lbrace\psi(\mathbf x,t)^*\frac{\partial}{\partial \mathbf x}\psi(\mathbf x,t)\right\rbrace.\tag{7}\label{eq7}
$$
This expression for the current is equivalent to OP's eq. (1). Note that it is only valid for special types of Hamiltonians. The general definition is \eqref{eq2b}.
Side note: the definitions for the currents in eqs. \eqref{eq2b}, \eqref{eq7} are not the only possibilities. In the case of eq. \eqref{eq7}, $\mathbf j$ can be regarded as an $(n-1)$-differential form, and any closed $(n-1)$-form can be added to it without invalidating the continuity equation.
[1] There may be a more standard reference out there, but I learned \eqref{eq2b} by reading about Pilot Wave theory from J. Bell, Beables for quantum field theory, in Speakable and unspeakable in quantum mechanics, Cambridge University Press, 1987.