With numpy:
In [128]: list_a = np.array([1, 2, 4, 6])
In [129]: filter = np.array([True, False, True, False])
In [130]: list_a[filter]
Out[130]: array([1, 4])
or see Alex Szatmary's answer if list_a can be a numpy array but not filter
Numpy usually gives you a big speed boost as well
In [133]: list_a = [1, 2, 4, 6]*10000
In [134]: fil = [True, False, True, False]*10000
In [135]: list_a_np = np.array(list_a)
In [136]: fil_np = np.array(fil)
In [139]: %timeit list(itertools.compress(list_a, fil))
1000 loops, best of 3: 625 us per loop
In [140]: %timeit list_a_np[fil_np]
10000 loops, best of 3: 173 us per loop