Scientific reports notified that the pandemic caused by the Coronavirus disease 2019 (COVID-19) has raised an unprecedented mental health emergency worldwide. Abrupt changes in daily routine, environmental constraints, adopted home confinement measures, and uncertainty about a date for returning to usual activities can potentially affect mental health and sports activities in athletes. Hence, we designed a cross-sectional study with a within-subjects design to investigate the impact of the pandemic on mental health, mood states, and life satisfaction of elite athletes. During the three phases of home confinement (April 14–24, n = 525), reopening (May 9–19, n = 464), and current semi-lockdown (July 20–31, n = 428), elite athletes voluntarily responded to an online survey. The self-report questionnaire was prepared to collect demographic and epidemiological variables of interest and the COVID-19-related information. All participants also completed the Profile of Mood State (POMS), General Health Questionnaire-28 (GHQ-28), and Satisfaction with Life Scale (SWLS). The main result is that the training rate, mental health, life satisfaction, and positive mood have decreased during the home confinement period as compared with the reopening and semi-lockdown phases. However, the need for psychosocial services has increased during the pandemic period. The present study provides the first preliminary evidence that home confinement conditions during the COVID-19 pandemic might have negatively influenced elite athlete’s mood state, mental health, and life satisfaction, as well as training rates. Monitoring the psychological parameters of elite athletes and developing strategies to improve their mental health during the COVID-19 pandemic should be on the agenda. Next studies, therefore, seem reasonable to focus on active interventions for athletes during the ongoing COVID-19 pandemic.