The loss is an increase on the $76 million loss a year earlier, as the global economic slowdown curbed sales and crimped margins.
Revenue for the period ended November 1st fell less than one per cent to $2.77 billion.
Sales at stores open at least a year, a key measure of retail health, dropped 0.3 per cent as consumers reined in purchases.
Toys R Us said last month that it had planned aggressive promotions for the Christmas period. Last year's fourth quarter generated about 42 per cent of full-year sales and all of its profit.