Despite successes in malaria control interventions over the past two decades, malaria remains a major public health concern. Over 125 million women live in endemic areas and experience adverse pregnancy outcomes due to malaria. Understanding health workers’ perspectives on malaria identification and management is important to informing policy changes on the control and eradication of the disease. This study explored the perspectives of health workers on malaria case identification and management among pregnant women in Savelugu Municipality, Ghana. A qualitative study with a phenomenology design was conducted among participants. Participants were purposively selected and interviewed using a semi-structured interview guide. Thematic analysis was performed and the results were presented as themes and sub-themes. Four themes and eight sub-themes regarding case identification and management of malaria in pregnancy were identified including malaria case identification training (trained and untrained), identification approach (signs/symptoms and routine laboratory test), diagnostic tools (rapid diagnostic test and microscopy) and management options. It revealed that attending malaria training programs was generally optional. Some of the participants had not undergone any refresher training for malaria identification after their formal training at health institutions. Participants identified malaria by its signs and symptoms. However, they often referred clients for routine laboratory tests for confirmation. When malaria is confirmed in pregnancy, quinine is used for first trimester treatment, while Artemisinin-based Combination Therapies are prescribed after the first trimester. Clindamycin was not used in the first trimester treatment. This study found that training programs were optional for health workers. Some participants have not received refresher training after graduating from health institutions. Treatment of confirmed cases did not include clindamycin for first trimester malaria infections. Malaria refresher training programs should be made mandatory for health workers. Every suspected case should be confirmed using Rapid Diagnostic Test or microscopy before treatment.