The performance of most pharmaceutical stocks has been underwhelming over the past year. The benchmark iShares US Pharmaceuticals ETF (NYSEMKT:IHE) has underperformed the S&P 500 by almost 20% in this time, and some companies in particular look especially cheap. Their share prices have not kept pace with the broader bull market, and that presents a bargain opportunity for investors.

Two big-name pharmaceuticals that have been making news a lot lately, much of that related to the COVID-19 pandemic, are Pfizer (NYSE:PFE) and Gilead (NASDAQ:GILD) (Pfizer with a vaccine in partnership with BioNTech, Gilead with a treatment called remdesivir). But while both have made COVID-related headlines, neither has seen a COVID-related boost -- both stocks are at a price-to-earnings ratio of less than 15, which is cheap from a valuation perspective in comparison to many peers. (Johnson & Johnson (NYSE:PFE) and Eli Lilly (NYSE:PFE) carry P/E ratios of 17.27 and 22.47 respectively.) But if we look to the future and past the pandemic, there is potential for both Pfizer and Gilead to produce great results for investors.

Working on vaccine

Image Source: Getty Images.

The case for Pfizer

Founded in 1849 in Brooklyn, Pfizer has had a remarkable journey. After 172 years, the company remains in the foreground of innovation and breakthrough in new drugs and therapeutics. Over the past few decades, Pfizer has been the name behind such well-known drugs and consumer products as Advil, Bextra, Diflucan, Viagra, Chapstick, and Preparation H. And during the coronavirus pandemic, Pfizer's vaccine with BioNTech was the first to be approved by the FDA (on Dec. 11).

As the world moves toward global inoculation, Pfizer stands to benefit with increasing revenue from this vaccine, which should bring in an estimated $15 billion in 2021 alone.  For full-year 2021 guidance, management estimated revenue of between $59.4 billion and $61.4 billion, meaning the vaccine should account for about a quarter of the total.

The company currently trades at a P/E of just 11.21 and offers investors a 4.3% dividend yield, much higher than the 1.37% average of the S&P 500 at this time. As mentioned before, Pfizer is trading at an extreme discount compared to its peers in the pharmaceutical space. With a bright future that I don't believe has been priced in yet by investors, this stock should be very tempting to add to portfolios.

The case for Gilead

Gilead Sciences joined many investors' watchlists (and portfolios) thanks to its COVID-19 treatment, remdesivir, which was approved Oct. 22 by the U.S. Food and Drug Administration. Within a month, though, the World Health Organization issued advice against using remdesivir, saying there was no evidence it improved survival or patient outcomes. Since then, the stock has languished around the $65 range. Despite the WHO announcing that Remdesivir does not do much to improve health of patients battling COVID-19, hospitals do continue to use it to treat patients in countries including India and Korea with moderate and severe infections. 

This was especially unfortunate given that, besides its efforts against COVID, the company seems to be in a tight spot. Its drug Biktarvy, a medicine to treat HIV, is its only product with increasing revenue in the past few years, with sales up 53% from 2019 to 2020. However, the company's other big names are flat or down, with Genvoya (for HIV) down 15%, Odefsy (for HIV-1) flat, and sofosbuvir (for hepatitis C) down 19% from 2019 to 2020.

However, there is some good news as well -- the company looks to be expanding its business into new markets with the acquisition of a biotech company called Forty Seven. On March 10, Gilead committed buying all outstanding shares of FortySeven in an all-cash deal at a hefty $95 a share, which came to a $4.9 billion acquisition price.

This move will help expand the company into cancer-fighting drugs, including magrolimab, an investigational monoclonal antibody that is being used against myelodysplastic syndrome, more often known as preleukemia. While the FDA has granted this drug fast-track status, hopefully meaning success for Gilead down the line, the future is still uncertain. While Gilead boasts a great 4.29% dividend yield, its P/E of only 9.26 looks to be discounted for a reason.

There is still tremendous uncertainty for future applications of remdesivir in relation to COVID-19. And the stagnation and decline in most of its core products is a concern. While we could see Biktarvy's growth expand enough to possibly offset the decline in its other products, the future is very unclear. One bright spot is the newly acquired magrolimab, which has been very successful in clinical trials and is classified as "first in-class." This drug could generate meaningful returns sometime in the future.

Which stock should you buy?

Both Pfizer and Gilead seem stable coming out of the pandemic, but the former appears far more likely to provide investors with superior returns into the future. Both companies are trading at very cheap valuations -- but in Gilead's case, that's justified, as an investment there will require a lot of faith in management to navigate out of the current tight spot. Pfizer, however, is a stable business with a lot more potential to build out its vaccine business into the future.

Pfizer announced March 23 that it plans to build out its mRNA vaccine business by itself and sees massive potential in this new venture. Pfizer's current vaccines business, which includes its pneumonia vaccine Prevnar 13, brought in nearly $6.58 billion, or about 16% of the drugmaker's total sales last year.  Pfizer is a stock that provides investors with a vision for the future and currently seems to be the better buy right now

This article represents the opinion of the writer, who may disagree with the “official” recommendation position of a Motley Fool premium advisory service. We’re motley! Questioning an investing thesis -- even one of our own -- helps us all think critically about investing and make decisions that help us become smarter, happier, and richer.