You need not to take a loop, you can straight away use the logical indexing.
ZEE=xlsread('zee.xlsx','Area','B2:MP138');
ZEE=ZEE';
A=load('daya50MW.txt');
B=load('dayaelninoMW.txt');
daya50zee = NaN(size(A)) ;
dayaelninozee = NaN(size(A)) ;
daya50zee(ZEE == 1) = A(ZEE == 1) ;
dayaelninozee(ZEE == 1) = B(ZEE == 1) ;