Empathy is a multidimensional construct and comprises the ability to perceive, understand and feel the emotional states of others. Gender differences have been reported for various aspects of emotional and cognitive behaviors including theory of mind. However, although empathy is not a single ability but a complex behavioral competency including different components, most studies relied on single aspects of empathy, such as perspective taking or emotion perception. To extend those findings we developed three paradigms to assess all three core components of empathy (emotion recognition, perspective taking and affective responsiveness) and clarify to which extent gender affects the neural correlates of empathic abilities. A functional MRI study was performed with 12 females (6 during their follicular phase, 6 during their luteal phase) and 12 males, measuring these tasks as well as self-report empathy questionnaires. Data analyses revealed no significant gender differences in behavioral performance, but females rated themselves as more empathic than males in the self-report questionnaires. Analyses of functional data revealed distinct neural networks in females and males, and females showed stronger neural activation across all three empathy tasks in emotion-related areas, including the amygdala. Exploratory analysis of possible hormonal effects indicated stronger amygdala activation in females during their follicular phase supporting previous data suggesting higher social sensitivity and thus facilitated socio-emotional behavior. Hence, our data support the assumption that females and males rely on divergent processing strategies when solving emotional tasks: while females seem to recruit more emotion and self-related regions, males activate more cortical, rather cognitive-related areas.