BMO Capital Markets downgraded Pfizer to market perform and told clients that the drugmaker faces "significant headwinds" in the next two years that will be marked by slower revenue and weaker multiple expansion.

Analyst Alex Arfaei wrote in a note published Wednesday that until Pfizer can turn over its product pipeline, shares of the pharmaceutical giant should take a breather from their strong run of the last 12 months.

"Our forecasts are in line with management's expectations of mid-single (digit) growth after 2020, coupled with margin expansion, and we remain bullish on a number of pipeline assets," Arfaei wrote. "However, these seem mostly reflected in the stock, and near-term headwinds may not allow for meaningful multiple expansion in 2019."

The BMO analyst highlighted higher immuno-oncology research and development as well as disappointing sales from Prevnar (lower adult sales), Ibrance (lower U.S. sales), Xtandi and Xeljanz (lower price) as just a few of the headwinds the New York-based Pfizer is likely to endure until the second half of 2020.

Pfizer, which develops and commercializes a variety of medicines and vaccines, has seen its stock rally 22 percent during the past year after it started highlighting its "underappreciated" drug pipeline, Arfaei wrote. That has helped the Dow-component change the narrative on Wall Street about its R&D productivity and its dependence on mergers and acquisitions for growth.

Still, Arfaei sees the pharmaceutical company's stock rising only to $46 over the next 12 months, 6 percent upside from Wednesday's close. The stock was up 1.5 percent Thursday afternoon.