The answer is no in general. Recall that if $T:X\longrightarrow Y$ is a surjective operator, then $X/{\rm ker}(T)$ is isomorphic to $Y$. The question may thus be equivalently stated: Let $X$ be a separable Banach and $Y$ a subspace of $X$. Does there exist a subspace $Z\subseteq X$ such that $X/Z$ is isomorphic to $Y$?
The answer is of course yes if $X$ is isomorphic to $\ell_2$. It is also yes if $X$ contains a complemented subspace isomorphic to $\ell_1$, because $\ell_1$ is surjectively universal for the class of separable Banach spaces (that is, $\ell_1$ admits a surjective operator onto any separable Banach space, and in particular onto any of its subspaces).
For a counterexample, let us look at the opposite phenomenon to the surjective universality property enjoyed by $\ell_1$; more precisely, let us consider a space that is injectively universal for the class of separable Banach spaces: every separable Banach space is (isometrically) isomorphic to a subspace of $C([0,1])$ (the Banach-Mazur theorem). So, if the OP's question were to have an affirmative answer, it would have to be the case that every separable Banach space is isomorphic to a quotient of $C([0,1])$; this is false.
Non-reflexive counterexamples: Let $Y$ be a nonreflexive subspace of $C([0,1])$ such that $c_0$ is not isomorphic to a subspace of $Y$ (e.g., $\ell_1$, the James space, and many others). Then there is no surjective operator from $C([0,1])$ onto $Y$. Indeed, a classical result of Pelczynski (see, e.g., p.119 of the book Topics in Banach space theory by Albiac and Kalton) tells us that non-weakly compact operators from $C(K)$ spaces fix a copy of $c_0$, and the claimed counterexample follows since a surjective operator onto a non-reflexive space is non-weakly compact.
Reflexive counterexamples: Every reflexive quotient of a $C(K)$ space is super-reflexive; this theorem is due to H.P. Rosenthal, who showed that a reflexive quotient of a $C(K)$ space is isomorphic to a quotient of $L_q(\mu)$ for some probability measure $\mu$ and $2\leq q<\infty$ (Corollary 11 of On subspaces of $L_p$, Ann. Math. 97 (1973), p.344-373) (Remark: it is true more generally that every reflexive quotient (in the Banach space sense) of a $C^\ast$-algebra is super-reflexive; this is due to Jarchow, On weakly compact operators on $C^\ast$-algebras, Math. Ann. 273 (1986), p.341-343). So, take $Y$ to be any reflexive subspace of $C([0,1])$ that is not super-reflexive. Then there is no surjective operator onto $Y$. For example, take $Y$ to be a subspace of $C([0,1])$ isomorphic to $(\bigoplus_{n=1}^\infty\ell_q^n)_{\ell_p}$, where $1<p<\infty$ and $q\in\{ 1,\infty\}$.
More reflexive counterexamples: let $1\leq p<\infty$. Then $\ell_p$ is isomorphic to a quotient of $C([0,1])$ if and only if $p\geq2$. Thus any subspace $Y$ of $C([0,1])$ such that $Y$ is isomorphic to $\ell_p$, for some $1<p<2$, is not a quotient of $C([0,1])$. (The fact that every operator from $C(K)$ to $\ell_p$ is compact whenever $1\leq p<\infty$ is Exercise 6.10 in the aforementioned book of Albiac and Kalton. Since $C([0,1])^{\ast\ast}$ is isomorphic to a space $L_\infty(\mu)$ for a suitable measure $\mu$, and since $\ell_p$ is reflexive for $1<p<2$, for the case $1<p<2$ it suffices to show that every operator from an $L_\infty(\mu)$ space to $\ell_p$ is compact whenever $1<p<2$; for some discussion of this see Remark 2 on p.211 of H.P. Rosenthal, On quasi-complemented subspaces of Banach spaces, with an appendix on compactness of operators from $L^p(\mu)$ to $L_r(\nu)$, J. Funct. Anal. 4 (1969), p. 176-214).