The meeting will take place at 5:00pm (1500 GMT), European Commission spokesman Margaritis Schinas said on Twitter.
Sturgeon will also meet the president of the European Parliament Martin Schulz and the heads of political groupings in the assembly.
However, European Council President Donald Tusk has refused to meet with the first minister as it is “not the appropriate moment”, a source in the council said on Tuesday.
Neither Schulz nor Juncker plan to hold press conferences after the talks, which come amid a tense atmosphere following Britain’s June 23 referendum.
Britain as a whole voted by 52 percent to 48 percent to leave the EU but Scotland voted strongly for Britain to remain — by 62 percent to 38 percent.
Europe’s leaders meet Wednesday without Britain for the first time following its shock vote.
Sturgeon said on Tuesday she was “utterly determined” to protect Scotland as she obtained a formal mandate for direct talks with the European Union institutions at an emergency session of the Scottish parliament.
“Tomorrow I will make an initial visit to Brussels to set out Scotland’s position and interests” to European Parliament leaders, Sturgeon said.
“Through all of this I am determined, utterly determined, to preserve Scotland’s relationship and place within the EU,” said Sturgeon, head of the pro-independence Scottish National Party (SNP).
Scotland is to draw up legislation for a new independence referendum to ensure it could be held during any negotiations for Britain to leave the EU, which would last a maximum of two years unless all EU member states agreed to extend them.
Outgoing Prime Minister David Cameron has rejected Sturgeon’s initiative, saying Scots had already voted against independence in 2014, and the referendum would require the authority of the British parliament to go ahead.
“The last thing Scotland needs now is another divisive referendum,” his spokeswoman said earlier.
But Sturgeon stressed the circumstances had changed since 2014 and Scotland was in “uncharted territory” and that a new referendum was now “highly likely”.