In full one-loop generality and in next-to-leading order in QCD, we studyrare top to Higgs boson flavour changing decay processes $t\to q h$ with$q=u,c$ quarks, in the general MSSM with R-parity conservation. Our primarygoal is to search for enhanced effects on $Br(t\to q h)$ that could be visibleat current and high luminosity LHC running. To this end, we perform ananalytical expansion of the amplitude in terms of flavour changing squark massinsertions that treats both cases of hierarchical and degenerate squark massesin a unified way. We identify two enhanced effects allowed by variousconstraints: one from holomorphic trilinear soft SUSY breaking terms and/orright handed up squark mass insertions and another from non-holomorphictrilinear soft SUSY breaking terms and light Higgs boson masses. Interestingly,even with $\mathcal{O}(1)$ flavour violating effects in the, presentlyunconstrained, up-squark sector, SUSY effects on $Br(t\to q h)$ come out to beunobservable at LHC mainly due to leading order cancellations between penguinand self energy diagrams and the constraints from charge- and colour-breakingminima (CCB) of the MSSM vacuum. An exception to this conclusion may be effectsarising from non-holomorphic soft SUSY breaking terms in the region where theCP-odd Higgs mass is smaller than the top-quark mass but this scenario isdisfavoured by recent LHC searches. Our calculations for $t\to q h$ decay aremade available in SUSY_FLAVOR numerical library.