simply pass your entire code as an argument of timeit:
import timeit
print(timeit.timeit(
"""
limit = 10000
prime_list = [i for i in range(2, limit+1)]
for prime in prime_list:
for elem in range(prime*2, max(prime_list)+1, prime):
if elem in prime_list:
prime_list.remove(elem)
"""
, number=10))