(Adds analyst comment, Biohaven CEO comment, shares)

Nov 9 (Reuters) - Pfizer Inc will acquire overseas marketing rights to two migraine drugs from Biohaven Pharmaceutical Holding Co for up to $1.24 billion, the companies said on Tuesday.

The deal includes an upfront payment of $500 million for the rights to Biohaven's rimegepant and zavegepant, with $150 million in cash and $350 million for the purchase of Biohaven equity at a 25% market premium.

Biohaven will also be able to fetch another $740 million in milestone payments and receive double-digit royalties on the drugs' overseas net sales from Pfizer.

Shares of Biohaven fell nearly 13% after the announcement.

Investors are likely disappointed that a pact for an outright sale of the company was not reached, Cowen analyst Ken Cacciatore said in a client note.

"The deal actually puts us in a stronger position because we have not given up any U.S. rights whatsoever on this asset (rimegepant)," Biohaven Chief Executive Officer Vlad Coric said.

Rimegepant, marketed as Nurtec ODT in the United States, was approved last year for the acute treatment of migraine attacks and it won expanded approval for the prevention of migraine episodes this May.

Biohaven is awaiting the European Medicines Agency's decision on the drug in the first half of 2022, after it was approved in the Middle East and Israel.

The company also expects to file for regulatory approval in other markets like China next year, Coric said.

Nurtec ODT brought in sales of about $136 million in the quarter ended Sept. 30, a 46% jump over the previous three months.

Zavegepant is being studied as an intranasal and a soft-gel formulation in late-stage clinical trials for migraine. (Reporting by Manojna Maddipatla in Bengaluru; Editing by Krishna Chandra Eluri and Aditya Soni)