It is unclear however whether both will be able to take their seats as MEPs.
Puigdemont lives in self-exile in Belgium and is wanted by Spain, while Junqueras is behind bars as a trial over his and 11 others' role in the failed secession attempt in October 2017 takes place in Madrid.
Both are locked in a power struggle to take leadership of the pro-independence movement in the northeastern region.
Puigdemont's list for Europe was the most voted in Catalonia.
The map shows Catalonia as a dark blue corner where Catalan separatist parties won the most votes.
Junqueras's ERC party, meanwhile, was part of a coalition of other separatist groupings in the Basque Country and Galicia in a joint list for Europe.
That alliance gained three MEPS, or 5.8 percent of the vote, while Puigdemont's Free for Europe list took two seats with 4.6 percent.
What happens next is unclear.
Under Spanish rules, all of those elected to the European Parliament first have to swear they will abide by Spain's constitution, a necessary move for the national electoral board to confirm them as MEPs.
That has to be done in person.
If Puigdemont came to Spain, he would immediately be arrested on a charge of rebellion.
Puigdemont, however, insists he will have immunity as soon as he is elected and that he doesn't in any case have to come to Spain to be confirmed as MEP.
Junqueras faces a sentence of up to 25 years in jail if found guilty of rebellion and misuse of public funds.
He would have to get permission from the Supreme Court that is trying him to travel to the European Parliament.