Use Python to remove lines in a files that start with an octothorpe?

This seems like a straight-forward question but I can't seem to pinpoint my problem. I am trying to delete all lines in a file that start with an octothorpe (#) except the first line. Here is the loop I am working with:

for i, line in enumerate(input_file):
    if i > 1:
        if not line.startswith('#'):
            output.write(line)

The above code doesn't seem to work. Does anyone known what my problem is? Thanks!