If you don't want to use the xmlrpclib's Binary class, you can just use the .encode() method of strings:

a = open("pdf_reference.pdf", "rb").read().encode("base64")

From my understanding base64decode only takes in a base64 string and looks like you have some headers on your string that are not encoded.

I would remove "data:application/pdf;base64,"

check out the doc here: https://docs.python.org/2/library/base64.html

When I've used it in the past, I have only used the encoded string.

base64.decode(,) takes files as args. you want to try

fout.write(base64.decodestring(code))

though your code example is not encoded. Here's a working example:

#!/usr/bin/python
import base64, os
code = 'TXkgYmluYXJ5IHN0cmluZw==\n'
with open(os.path.expanduser('~/Desktop/test.pdf'), 'wb') as fout:
     fout.write(base64.decodestring(code))

I had a similar problem. I used the following function to generate and return a PDF file from a base64 encoded string in Django. (Tested only with Python 3.5)

def b64_to_pdf(b64content):
    import io as BytesIO
    import base64
    from django.http import HttpResponse

    buffer = BytesIO.BytesIO()
    content = base64.b64decode(b64content)
    buffer.write(content)

    response = HttpResponse(
        buffer.getvalue(),
        content_type="application/pdf",
    )
    response['Content-Disposition'] = 'inline;filename=some_file.pdf'
    return response

If you are not using Django, then you just need to figure out how to return the PDF file in a view or something like that. I use HttpResponse that handles various things for the response.

I can also use this function for any kind of b64 encoded string, so it's reusable across the project.

As @pvg mentioned in the comments, overriding load_resource function with your base64 functionality does the trick.

import base64,io

def load_resource(self, reason, filename):
    if reason == "image":
        if filename.startswith("http://") or filename.startswith("https://"):
            f = BytesIO(urlopen(filename).read())
        elif filename.startswith("data"):
            f = filename.split('base64,')[1]
            f = base64.b64decode(f)
            f = io.BytesIO(f)
        else:
            f = open(filename, "rb")
        return f
    else:
        self.error("Unknown resource loading reason \"%s\"" % reason)

EDIT :

This is a sample code to insert images into pdf. I commented some instructions in code.

from fpdf import FPDF
import os
import io
import base64


class PDF(FPDF):

    def load_resource(self, reason, filename):
        if reason == "image":
            if filename.startswith("http://") or filename.startswith("https://"):
                f = BytesIO(urlopen(filename).read())
            elif filename.startswith("data"):
                f = filename.split('base64,')[1]
                f = base64.b64decode(f)
                f = io.BytesIO(f)
            else:
                f = open(filename, "rb")
            return f
        else:
            self.error("Unknown resource loading reason \"%s\"" % reason)


    def sample_pdf(self,img,path):

        self.image(img,h=70,w=150,x=30,y=100,type="jpg")
        #make sure you use appropriate image format here jpg/png
        pdf.output(path, 'F')

if __name__ == '__main__':
    img = # pass your base64 image
    # you can find sample base64 here : https://pastebin.com/CaZJ7n6s

    pdf = PDF()
    pdf.add_page()
    pdf_path = # give path to where you want to save pdf
    pdf.sample_pdf(img,pdf_path)