Ackman chopped his stake in the Canadian drugmaker to 8.5 percent from 9.9 percent. In a filing, he said the shares were sold in order to "generate a tax loss" for investors.
Pershing's Valeant investment suffered this year, as the company's stock plunged about 29 percent amid concerns about its business model and drug pricing. Ackman has staunchly defended Valeant in the past, and even increased his stake earlier this year.
As of Wednesday, Pershing Square had lost about 20 percent on the year.
This month, Valeant cut its revenue and profit forecasts for 2015. But the company noted it expected double-digit sales growth next year through higher volume.
Valeant shares fell about 0.7 percent in extended trading Thursday.
— Reuters contributed to this report.