You can add a persistent variable and check if it is empty. If it is empty, then it means it is the first time the Matlab function block is being executed, in which case you can set the output to be zero.
Example code:
function y = fcn(u)
persistent x
if isempty(x)
x = 1;
end
if (x==1)
y = 0; %y is 0 on the first simulation time step
else
y = 1; %y is 1 on for the rest
end
