A junction object is as good as any other custom object. Use the api name of the object in your SOQL and the fields on the object. E.g., if Account_Contact__c is a junction object, you can use to fetch results by writing a query on the object as - select <fields> from account_contact__c <where clause>
Please refer the below link to get junction object queries - https://developer.salesforce.com/forums/?id=906F00000008o7tIAA
Thanks,
Selva