Assuming the child object name as ChildObjectName__c
and lookup API name on child isLookupName__c
, your query with where clause would look as:
SELECT Id,
(SELECT Checkbox__c FROM ChildRelationshipName__r)
FROM Parent__c WHERE
Id IN (SELECT LookupName__c FROM ChildObjectName__c WHERE checkbox__c = true)
Related documentation for reference: Basic SOQL Relationship Queries. Similar query with Account and Contact object:
SELECT Name, (SELECT Name FROM Contacts)
FROM Account WHERE
Id IN (SELECT AccountId FROM Contact)