The way to do this in pygame is to use pygame.time.set_timer() and have an event generated every given number of milliseconds. This will allow the event to be handled in the script's main loop like any other. 
Here's a somewhat boring, but runnable, example of doing something like that:
import pygame
pygame.init()
SIZE = WIDTH, HEIGHT = 720, 480
FPS = 60
BLACK = (0,0,0)
WHITE = (255,255,255)
GREEN = (0,255,0)
RED = (255,0,0)
BLUE = (0,0,255)
BACKGROUND_COLOR = pygame.Color('white')
screen = pygame.display.set_mode(SIZE)
clock = pygame.time.Clock()
font = pygame.font.SysFont('', 30)
COOKIE_EVENT = pygame.USEREVENT
pygame.time.set_timer(COOKIE_EVENT, 1000)  # periodically create COOKIE_EVENT
class Player(pygame.sprite.Sprite):
    def __init__(self, position):
        super(Player, self).__init__()
        self.cookie_count = 0
        self.grandma = 10 # grandma bakes 10 cookies/second
        text = font.render(str(self.cookie_count), True, RED, BLACK)
        self.image = text
        self.rect = self.image.get_rect(topleft=position)
        self.position = pygame.math.Vector2(position)
        self.velocity = pygame.math.Vector2(0, 0)
        self.speed = 3
    def update_cookies(self):
        self.cookie_count += self.grandma  # 10 cookies per grandma
        if self.cookie_count > 499:
            self.cookie_count = 0
        text = font.render(str(self.cookie_count), True, RED, BLACK)
        self.image = text
player = Player(position=(350, 220))
running = True
while running:
    clock.tick(FPS)
    for event in pygame.event.get():
        if event.type == pygame.QUIT:
            running = False
        if event.type == COOKIE_EVENT:
            player.update_cookies()
        keys = pygame.key.get_pressed()
        if keys[pygame.K_LEFT]:
            player.velocity.x = -player.speed
        elif keys[pygame.K_RIGHT]:
            player.velocity.x = player.speed
        else:
            player.velocity.x = 0
        if keys[pygame.K_UP]:
            player.velocity.y = -player.speed
        elif keys[pygame.K_DOWN]:
            player.velocity.y = player.speed
        else:
            player.velocity.y = 0
        player.position += player.velocity
        player.rect.topleft = player.position
    screen.fill(BACKGROUND_COLOR)
    screen.blit(player.image, player.rect)
    pygame.display.update()