Abstract Background In patients with a total cavopulmonary connection in Fontan circulation, the access to the common atrium (CA) during a catheter ablation can be challenging, even in the presence of fenestration in an intra-atrial lateral tunnel (IALT). In our department, the fenestration is typically marked with metal clips (MCs). To the best of our knowledge, there is no previous report of balloonoplasty of clipped fenestration. Case summary A 19-year-old male with hypoplastic left heart syndrome (HLHS) was scheduled for catheter ablation of recurrent atrial tachycardia. He was diagnosed with HLHS prenatally and underwent a stepwise surgical palliation. Fontan circulation was completed with the creation of a fenestrated IALT. The fenestration was marked by four MCs. During the ablation procedure, the passage of the steerable sheath with mapping catheter to the CA was prevented by a small fenestration size and rigidness of the edges of the fenestration caused by the MCs. Multiple attempts to dilate the fenestration using a peripheric angioplasty balloon failed. Only angioplasty with the ‘balloon-against-dilator’ technique was finally successful. Activation map showed a counterclockwise atrial flutter in the CA; successful ablation was performed. Discussion We present a case of challenging access to the CA through a clipped fenestration in a polytetrafluoroethylene baffle for atrial tachycardia ablation. Even though a tunnel fenestration in Fontan patients facilitates access to the CA, the passage of a steerable introducer with a mapping catheter may be challenging due to diameter mismatch and the rigidity of its edges caused by MCs. The balloon-against-dilator technique might be helpful when conventional balloon angioplasty fails.