In this present work, the authors obtain Fekete-Szeg$\ddot{o}$ inequality for certain normalized analytic function $f(z)$ defined on the open unit disk for which $$\frac{{\lambda}{\beta}z^3(L(a,c)f(z))^{{\prime}{\prime}{\prime}}+(2{\lambda}{\beta}+{\lambda}-{\beta})z^2(L(a,c)f(z))^{{\prime}{\prime}}+z(L(a,c)f(z))^{{\prime}}}{{\lambda}{\beta}z^2(L(a,c)f(z))^{{\prime}{\prime}}+({\lambda}-{\beta})z(L(a,c)f(z))^{\prime}+(1-{\lambda}+{\beta})(L(a,c)f(z))}\;(0{\leq}{\beta}{\leq}{\lambda}{\leq}1)$$ lies in a region starlike with respect to 1 and is symmetric with respect to the real axis. Also certain applications of the main result for a class of functions defined by Hadamard product (or convolution) are given. As a special case of this result, Fekete-Szeg$\ddot{o}$ inequality for a class of functions defined through fractional derivatives are obtained.