Objectives: To develop an evidence-based guideline for the non-pharmacological management of persistent headaches associated with neck pain (i.e., tension-type or cervicogenic). Methods: This guideline is based on systematic reviews of high-quality studies. A multidisciplinary expert panel considered the evidence of clinical benefits, cost-effectiveness, societal and ethical values, and patient experiences when formulating recommendations. Target audience includes clinicians; target population is adults with persistent headaches associated with neck pain. Results: When managing patients with headaches associated with neck pain, clinicians should (a) rule out major structural or other pathologies, or migraine as the cause of headaches; (b) classify headaches associated with neck pain as tension-type headache or cervicogenic headache once other sources of headache pathology has been ruled out; (c) provide care in partnership with the patient and involve the patient in care planning and decision making; (d) provide care in addition to structured patient education; (e) consider low-load endurance craniocervical and cervicoscapular exercises for tension-type headaches (episodic or chronic) or cervicogenic headaches >3 months duration; (f) consider general exercise, multimodal care (spinal mobilization, craniocervical exercise and postural correction) or clinical massage for chronic tension-type headaches; (g) do not offer manipulation of the cervical spine as the sole form of treatment for episodic or chronic tension-type headaches; (h) consider manual therapy (manipulation with or without mobilization) to the cervical and thoracic spine for cervicogenic headaches >3 months duration. However, there is no added benefit in combining spinal manipulation, spinal mobilization and exercises; and (i) reassess the patient at every visit to assess outcomes and determine whether a referral is indicated. Conclusions: Our evidence-based guideline provides recommendations for the conservative management of persistent headaches associated with neck pain. The impact of the guideline in clinical practice requires validation. Significance: Neck pain and headaches are very common comorbidities in the population. Tension-type and cervicogenic headaches can be treated effectively with specific exercises. Manual therapy can be considered as an adjunct therapy to exercise to treat patients with cervicogenic headaches. The management of tension-type and cervicogenic headaches should be patient-centred.