Background: Neck pain is a frequent complaint in office workers. This pain can be caused by myofascial trigger points (MTrPs) in the trapezius muscle. This study aimed to determine the effectiveness of deep dry needling (DDN) of active MTrPs in the trapezius muscle. Methods: A randomized, single blinded clinical trial was carried out at the Physical Therapy Department at Physiotherapy in Women's Health Research Group at Physical Therapy Department of University of Alcalá, in Alcalá de Henares, Madrid, Spain. Forty-four office workers with neck pain and active MTrPs in the trapezius muscle were randomly allocated to either the DDN or the control group (CG). The participants in the DDN group were treated with DDN of all MTrPs found in the trapezius muscle. They also received passive stretch of the trapezius muscle. The CG received the same passive stretch of the trapezius muscle only. The primary outcome measure was subjective pain intensity, measured using a visual analogue scale (VAS). Secondary outcomes were pressure pain threshold (PPT), cervical range of motion (CROM) and muscle strength. Data were collected at baseline, after interventions and 15 days after the last treatment. Results: Differences were found between the DDN group and the CG for the VAS (P < 0.001), PPT (P < 0.001), range of motion (AROM) (P < 0.05) and strength (P < 0.05) after intervention and at the 15-day follow-up. Discussion: Deep dry needling and passive stretch seems to be more effective than passive stretch only. The effects are maintained in the short term. The results support the use of DDN in the management of trapezius muscle myofascial pain syndrome in neck pain.