MySQL 8.0

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CREATE TABLE course (id INTEGER);
CREATE TABLE enrol (course_id  INTEGER);
INSERT INTO course VALUES (1), (2), (3);

Records: 3  Duplicates: 0  Warnings: 0

INSERT INTO enrol VALUES (1), (1), (1), (2);

Records: 4  Duplicates: 0  Warnings: 0

SELECT * FROM course;

id

1

2

3

SELECT * FROM enrol;

course_id

1

1

1

2

DELETE c, e
FROM course c
LEFT JOIN enrol e ON e.course_id = c.id
LEFT JOIN (SELECT course_id, COUNT(*) count FROM enrol GROUP BY course_id) t
ON t.course_id = c.id
WHERE e.course_id IS NULL OR t.count < 3;
SELECT * FROM course;

id

1

SELECT * FROM enrol;

course_id

1

1

1