We aimed to explore the engagement of fathers in a community-based group intervention (Juntos) for children with congenital Zika syndrome (CZS) and their caregivers in Brazil. Six Juntos groups were facilitated from August 2017 to May 2018. We conducted a qualitative study to evaluate the feasibility and acceptability of the intervention for fathers of children with CZS. Methods included participant observation, focus group discussions, and semi-structured interviews of fathers with a child enrolled in the program. Data collected were transcribed, coded and thematically analyzed to explore father preference for, and beliefs about the intervention and to assess potential barriers and enablers to their involvement. Forty-nine families (61 participants) enrolled, of whom 20% (12/61) were fathers. Seven (58%) fathers attended more than 7 out of 10 sessions. The content of Juntos was found to be acceptable to those fathers who attended. Participation in the group offered fathers the opportunity to share experiences of caring for their child and demonstrate their importance as care agents. Work commitments, and the view of mothers as primary caregivers were barriers to engagement of fathers. Facilitators to engagement included a presentation of clear objectives for fathers' involvement and the opportunity to learn a practical skill related to caring for their child. A better understanding of the perspectives of fathers is crucial to help increase their involvement in parenting interventions.