A simple ruby script to get a list of orgs and the user count for each.

fetch_user_count_by_org.rb

#!/usr/bin/env ruby

require 'octokit'
require 'json'

client = Octokit::Client.new(access_token: ENV['GITHUB_TOKEN'])

query = <<-GRAPHQL
query { 
  enterprise(slug: "<MY-ENT-NAME>"){ 
    organizations(first: 100){ 
      nodes{
        name
      }
    }
  }
}
GRAPHQL

enterprises = client.post '/graphql', { query: query }.to_json

puts enterprises.data.enterprise.organizations.nodes.inspect

enterprises.data.enterprise.organizations.nodes.each do |org|
  puts org.name
  org_data = client.org_members(org.name)
  puts org_data.count
end

Usage:

Replace your enterprise slug on line 10.

gem install octokit
gem install json

export GITHUB_TOKEN=<My-Super_secret-Token!>

ruby fetch_user_count_by_org.rb