<B>Edit.</B>  I decided to add a little more explanation to make the result "sharp".  For a smooth, projective scheme $X$ over an algebraically closed field $k$, for every finitely presented, flat, dominant morphism $p:Y\to X$, the kernel of the pullback homomorphism,
$$
p^*:\text{Pic}(X)\to \text{Pic}(Y),
$$
is a finitely generated subgroup.  This result is "sharp" in the sense that every finitely generated subgroup is of the form $\text{Ker}(p^*)$ for a smooth, surjective morphism $p$.  One step in finite generatedness of $\text{Ker}(p^*)$ is finite generatedness of the quotient group, $\text{Pic}(X)/\text{Pic}^0(X)$.  The result, the "Theorem of the Base" of Lang and N&eacute;ron, is quite involved, whereas the consequence to the OP's question follows already from finite generatedness of the intersection $\text{Pic}^0(X)[p]$ of $\text{Ker}(p^*)$ and the subgroup $\text{Pic}^0(X)$.  This is much easier.

To prove that $\text{Pic}^0(X)[p]$ is finitely generated, the main reduction is the proposition that every fppf cover of a quasi-compact scheme is "refined" by an fppf cover that is quasi-finite.  This is a Bertini hyperplane theorem that holds for arbitrary Noetherian schemes, not just smooth, projective $k$-schemes.  Thus, let $X$ be a Noetherian scheme, and let $p:Y\to X$ be a flat, finitely presented morphism.

<B>Proposition 1.</B>  There exists a morphism $i:Z\to Y$ that is a disjoint union of locally closed immersions such that the composition $q=p\circ i$ is flat, quasi-finite, and has image equal to the image of $p$.

<B>Proof.</B>  Since $p$ is flat and finitely presented, the image of $p$ is open.  Up to replacing $X$ by the open image of $p$, assume that $p$ is surjective.

The argument is essentially a Bertini hyperplane argument. First of all, up to replacing $Y$ by a disjoint union of open affine subschemes, assume that $Y$ is affine.  Denote by $Y_{\text{equi}}\subset Y$ the maximal open subset on which $p$ is (locally) equidimensional, i.e., at every point of every fiber of $p$, the irreducible components of the fiber containing the point all have equal dimensions.  The restriction of $p$ to $Y_{\text{equi}}$ is still surjective.  Thus, without loss of generality, assume that $p$ is (locally) equidimensional.  Then on every connected component $Y_\alpha$ of $Y$, the fiber dimension of $p$ is constant.  We construct $Z$ as a disjoint union of schemes $Z_\alpha$ where $i_\alpha:Z_\alpha\to Y_\alpha$ is a disjoint union of locally closed immersions such that $p_\alpha\circ i_\alpha$ is a quasi-finite, flat morphism with image equal to the image of $p_\alpha$.

Thus, without loss of generality, assume that $Y$ is equidimensional of dimension $d$.  The proof of the existence of $i:Z\to Y$ as above is by induction on $d$.  If $d$ equals $0$, then define $Z$ to equal $Y$.  Thus, by way of induction, assume that $d>0$ and assume the result is proved for $d-1$.  

Let $e:Y\hookrightarrow \mathbb{A}^n_X$ be a closed immersion of $X$-schemes.  For every point in the image of $p$, $x:\text{Spec}\ k \to X,$ the fiber $Y_x=p^{-1}(x)$ has only finitely many associated points.  For every linear polynomial $t_x$ in the coordinate ring $k[\mathbb{A}^n_k]=k[t_1,\dots,t_n]$ that vanishes at none of these finitely many associated points, multiplication by $t_x$ is injective on $\mathcal{O}_{Y_p}$.  Let $t\in\mathcal{O}_{X,x}[t_1,\dots,t_n]$ be an element mapping to $t_x$. Denote by $H$ the zero scheme of $t$.  

By the local flatness criterion, the intersection $H\cap Y$ is flat at $x$, cf. Theorem 22.5, p. 176, "Commutative ring theory", H. Matsumura, Cambridge studies in mathematics, vol 8.  By the usual arguments, there exists an open affine neighborhood of $x$ such that $t$ lifts to a section of the structure sheaf of $\mathbb{A}^n_X$ over this open.  Define $H$ to be the zero scheme of $t$ on this open.  By openness of the flat locus, etc., there exists an open subscheme $U$ of $Y$ containing $H\cap Y_x$ such that $H\cap U$ is flat over $X$.  Choosing $t_x$ so that $H\cap Y_x$ is nonempty, $U\cap H \to X$ has image containing $p$, and it is equidimensional of dimension $d-1$ (this last by Krull's Hauptidealsatz).  

Thus, by the induction hypothesis applied to $U\cap H \to X$, there exists a locally closed immersion $i_x:Z_x\to U\cap H$ such that $p\circ i_x$ is quasi-finite and flat with image $V_x$ containing $x$.  As we vary $x$, the open images $V_x$ cover $X$.  Since we assumed that $X$ is quasi-compact, finitely many of these opens suffice to cover $X$.  Define $i:Z\to Y$ to be the disjoint union of these finitely many locally closed immersions $i_x$.  Since the composition $p\circ i$ is quasi-finite and flat on each of the finitely many connected components, it is quasi-finite and flat.  By construction, the image equals the image of $p$.  Thus, the lemma is proved by induction on $d$. <B>QED</B>

<B>Lemma 2.</B>  Let $q:Z\to X$ be a quasi-finite, flat morphism that is dominant.  There exists a dense open subscheme $j:V\hookrightarrow X$ and a positive integer $n$ such that the kernel of the pullback homomorphism $q^*:\text{Pic}(X)\to \text{Pic}(Z)$ is contained in the kernel of the homomorphism $\text{Pic}(X)\xrightarrow{j^*}\text{Pic}(V)\xrightarrow{n\cdot -} \text{Pic}(V).$

<B>Proof.</B>
For every finitely presented, quasi-finite morphism $q:Z\to X$, there exists a dense open subset $V\subset X$ such that $q^{-1}(V)\to V$ is finite.  Since $q$ is dominant and flat, the morphism $q^{-1}(V)\to V$ is surjective, finite, and flat.  

There exists a norm map, $$\text{Nm}_q : \text{Pic}(q^{-1}(V))\to \text{Pic}(V), \ \ \mathcal{L} \mapsto \text{det}(q_*\mathcal{L})\otimes \text{det}(q_*\mathcal{O})^{\vee}.$$  This is described in detail in Mumford's <I>Lectures on curves on an algebraic surface.</I>  For every connected component $V_\alpha$ of $V$, the morphism $q$ has constant finite degree $m$ over that component. For every invertible sheaf $\mathcal{M}_\alpha$ on $V_\alpha$, $\text{Nm}_q(q^*\mathcal{M}_\alpha)$ equals $\mathcal{M}_\alpha^{\otimes m}$.  Thus, defining $n$ to equal the least common multiple of these integers $m$, for every invertible sheaf $\mathcal{M}$ on $V$, if $q^*\mathcal{M}$ is trivial, then also $\mathcal{M}^{\otimes n}$ is trivial.  Thus, for an invertible sheaf $\mathcal{M}$ on $X$, if $q^*\mathcal{M}$ is trivial, then also $j^*\mathcal{M}^{\otimes n}$ is trivial. <B>QED</B>

Now let $k$ be an algebraically closed field.  Let $X$ be a smooth, projective $k$-scheme.  The relative Picard functor $\text{Pic}_{X/k}$ is represented by a $k$-scheme whose connected components are projective.  In particular, the identity component $\text{Pic}^0_{X/k}$ is an Abelian variety over $k$.  The group of $k$-points, $\text{Pic}^0(X)$, is divisible and infinitely generated with finite $n$-torsion for every integer $n$.  

For every finitely presented, flat, dominant morphism $p:Y\to X$, denote by $\text{Pic}^0(X)[p]$ the kernel of the homomorphism, $$ \text{Pic}^0(X) \hookrightarrow \text{Pic}(X) \xrightarrow{p^*} \text{Pic}(Y). $$

<B>Proposition 3.</B>  For every finitely presented, flat, dominant morphism $p:Y\to X$, the kernel $\text{Pic}^0(X)[p]$ is a finitely generated Abelian subgroup of $\text{Pic}^0(X)$.  

<B>Proof.</B>  By Proposition 1, there exists a morphism $i:Z\to Y$ such that $q=p\circ i:Z\to X$ is flat, quasi-finite, and dominant.  The subgroup $\text{Pic}^0(X)[p]$ is contained in the subgroup $\text{Pic}^0_{X/k}[q]$.  Thus, to prove that $\text{Pic}^0(X)[p]$ is finitely generated, it suffices to prove that $\text{Pic}^0(X)[q]$ is finitely generated.  

By Lemma 2, there exists a dense open subset $j:V\hookrightarrow X$ and an integer $n$ such that the kernel of $q^*$ is contained in the kernel of $$\text{Pic}^0(X)\xrightarrow{j^*}\text{Pic}(V)\xrightarrow{n\cdot -}\text{Pic}(V).$$   The kernel $K$ of the restriction map $j^*:\text{Pic}(X)\to \text{Pic}(V)$ is generated by the finitely many irreducible components of $X\setminus V$ that have codimension $1$ in $X$.  The intersection $K^0$ of $K$ with the subgroup $\text{Pic}^0(X)$ is a subgroup of the finitely generated group $K$, hence also $K^0$ is finitely generated.  The quotient of $\text{Pic}^0(X)$ by $K^0$ still has finite $n$-torsion: since $\text{Pic}^0(X)$ is divisible, the inverse image $I$ in $\text{Pic}^0(X)$ of this $n$-torsion is an extension of $K^0$ by the $n$-torsion of $\text{Pic}^0(X)$.  As both of these groups are finitely generated, also $I$ is finitely generated.  Since $\text{Pic}^0(X)[q]$ is contained in the finitely generated group $I$, also $\text{Pic}^0(X)[q]$ is finitely generated.  <B>QED</B>

<B>Corollary 4.</B> For $p:Y\to X$ as in the previous proposition, the kernel of $p^*:\text{Pic}(X)\to \text{Pic}(Y)$ is a finitely generated Abelian group.

<B>Proof.</B> The quotient of $\text{Ker}(p^*)$ by $\text{Pic}^0(X)[p]$ is a subgroup of the N&eacute;ron-Severi group $\text{Pic}(X)/\text{Pic}^0(X)$.  By the "Theorem of the Base" of Lang and N&eacute;ron, the N&acute;ron-Severi group is finitely generated.  Thus, the subgroup is also finitely generated.  By the proposition, $\text{Pic}^0(X)[p]$ is finitely generated.  Thus, the extension group $\text{Ker}(p^*)$ is also finitely generated. <B>QED</B>

As mentioned at the top, the result is sharp in the following sense.

<B>Proposition 5.</B> For every integral, normal, locally factorial Noetherian scheme $X$, for every finitely generated Abelian subgroup $K$ of $\text{Pic}(X)$, there exists a smooth, surjective morphism $p:Y\to X$ such that $p^*:\text{Pic}(X)\to \text{Pic}(Y)$ is surjective with kernel equal to $K$.

<B>Proof.</B>  This is proved by induction on the minimum number of generators of $K$.  If $K$ is zero, then define $p$ to be the identity morphism.  Thus, by way of induction, assume that $K$ is nonzero, and assume that the result is proved whenever the number of generators is strictly smaller than the minimal number of generators of $K$.

Let $L$ be an invertible sheaf on $X$ whose class gives one of the generators in a minimal set of generators of $K$.  Denote by $\overline{p}:\overline{Y}\to X$ the projective space bundle that admits a universal invertible quotient, $\overline{p}^*(\mathcal{O}_X \oplus L) \to \mathcal{O}(1)$.  The two projections, $$a_1:\mathcal{O}_X\oplus L \to \mathcal{O}_X, \ \ a_2:\mathcal{O}_X\oplus L \to L,$$ are invertible quotients.  These define sections of $\overline{p}$, $$s_1,s_2:X\to \overline{Y},$$ whose images, $D_1$, resp. $D_2$, are disjoint, integral Cartier divisors.  Define $Y$ to be the open complement of $D_1\cup D_2$.  

The pullback homomorphism and the class of $\mathcal{O}(1)$ define a splitting of Abelian groups, $$\text{Pic}(X)\oplus \mathbb{Z}[\mathcal{O}(1)] \xrightarrow{\cong} \text{Pic}(\overline{Y}).$$  Since $Y$ is the open complement of a union of two disjoint Cartier divisors, the usual open-closed exact sequence gives, $$\mathbb{Z}[\mathcal{O}(D_1)] \oplus \mathbb{Z}[\mathcal{O}(D_2)] \to \text{Pic}(\overline{Y}) \to \text{Pic}(Y) \to 0. $$  Combined with the splitting, $\text{Pic}(Y)$ is isomorphic to the quotient of $\text{Pic}(X)$ by the class of $\mathcal{O}(D_1-D_2)$, i.e., the class of $L$.  Thus, $p^*$ is surjective and the kernel equals $\mathbb{Z}[L]$.  By the induction hypothesis, there exists a further smooth, surjective homomorphism to $Y$ such that the pullback map is surjective with kernel equal to $K/\mathbb{Z}[L]$.  Thus, the result is proved by induction on the minimal number of generators of $K$. <B>QED</B>