A contentious primary season has taken a toll on pro-Republican super PACs, which spent heavily on election battles among GOP candidates and are looking to November with less cash on hand than their Democratic counterparts.

The largest pro-Republican super PACs have not only raised less money than Democratic groups but spent a far larger share of it on primary fights, a Wall Street Journal analysis of campaign-finance filings shows. For the current campaign cycle through July 3, pro-Republican super PACs in the study directed...