Addition of boundary localised kinetic and Yukawa terms to the action of a 5-dimensional Standard Model would non-trivially modify the Kaluza-Klein spectra and some of the interactions among the Kaluza-Klein excitations compared to the minimal version of this model, in which, these boundary terms are not present. In the minimal version of this framework known as Universal Extra Dimensional model, special assumptions are made about these unknown, beyond the cut-off contributions to restrict the number of unknown parameters of the theory to a minimal. We estimate the contribution of Kaluza-Klein modes to the branching ratios of $B_{s(d)}rightarrowmu^{+}mu^{-}$ in the framework of non-minimal Universal Extra Dimensional, at one loop level. The results have been compared to the experimental data to constrain the parameters of this model. From the measured decay branching ratio of $B_s rightarrow mu^+ mu^-$ (depending on the values of boundary localised parameters) lower limit on $R^{-1}$ can be as high as 800 GeV. We have briefly reviewed the bounds on nmUED parameter space coming from electroweak precision observables. The present analysis ($B_s rightarrow mu^+ mu^-$) has ruled out new regions of parameter space in comparison to the analysis of electroweak data. We have revisited the bound on $R^{-1}$ in Universal Extra Dimensional model, which came out to be 454 GeV. This limit on $R^{-1}$ in Universal Extra Dimensional framework is not as competitive as the limits derived from the consideration of relic density or Standard Model Higgs boson production and decay to $W^+ W^-$. Unfortunately, $B_{d}rightarrowmu^{+}mu^{-}$ decay branching ratio would not set any significant limit on $R^{-1}$ in a minimal or non-minimal Universal Extra Dimensional model.
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