The answer is, as Noah suggests, negative.
Suppose that $\frak M$ is a model of $\sf ZFCU$ where $U$ is not a set. Consider the model generated by taking all the permutations of $U$ which are sets (namely, permutations of a subset of $U$, and therefore the identity elsewhere). And consider $\cal F$ to be the filter generated by $\langle\operatorname{fix}(E)\mid E\text{ finite set of atoms}\rangle$, where $\operatorname{fix}(X)$ is the pointwise stabilizer of a set. Let $\frak N$ be the permutation model defined from these, and I claim that:
- $\frak N\models\sf ZFCU$.
- $\frak N\not\models\sf SDC$.
To see (1) holds, first prove that every set of atoms in $\frak N$ is finite; that every transitive set in $\frak N$ contains only finitely many atoms; by induction on the rank of a set show that if $x$ is a transitive set and $E=x\cap U$, then $\operatorname{fix}(E)=\operatorname{fix}(x)$. In particular a classical theorem about permutation models is that if the pointwise stabilizer of a set is in the filter, then the set can be well-ordered.
To see that (2) holds, or rather that $\sf SDC$ fails, consider the statement $\phi(x,y)$ to be "If $x$ is a set of atoms, then $y$ is a set of atoms and $x\subsetneq y$". Of course every set of atoms can be extended to a larger set of atoms; but if $f$ exists as in the schema, then $\bigcup f(n)$ exists by replacement and union, but it has to be an infinite set of atoms.
Here is a tentative (better) example. I don't have time to work out all the details yet.
Start with a model of $\sf ZFCU$ where $U$ is not a set, and there is a bijection between $U$ and the ordinals. Let $F$ denote a definable class function from $U$ onto $\omega$ such that every fiber is a proper class. This is doable from the bijection with the ordinals, for example (which is really the only reason to require that bijection).
Now consider all the set permutations of $U$ which preserve $F$. Namely $\pi\colon U\to U$, which is the identity outside some set $d$, and $F(a)=F(\pi(a))$ for all $a\in d$.
Let $\cal F$ be the filter generated by $\{\operatorname{fix}(E)\mid E\text{ is any set of urelements and }F[E]\text{ is bounded in }\omega\}$. Let $\frak N$ be the permutation model.
- $\frak N\models\sf ZFCU$.
- $F$ is definable in $\frak N$.
- There is no $f\colon\omega\to U$ such that $F(f(n))=n$.
Now consider the formula $\phi(x,y)$ to be "If $x$ is a finite partial inverse of $F$ [read: $F(x(n))=n$ for $n\in\operatorname{dom}(x)$], then so is $y$, and $x\subsetneq y$". This is an obvious counterexample to $\sf SDC$ as in the previous case.