SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    13878, 13877, 13876, 13875, 13874, 13873, 
    13872, 13870, 13869, 13829, 13862, 
    13858, 13850, 13849, 13848, 13847, 
    13846, 13845, 13844, 13843, 13842, 
    13841, 13840, 13839, 13838, 13837, 
    13836, 13835, 13834, 13833, 13832, 
    13831, 13830, 13827, 13826, 13825, 
    13824, 13823, 13822, 13821
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00060

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_ult_product_prices range usergroup,product_id,company_id,lower_limit,usergroup_id usergroup 13 1 Using where