Chronic anal fissure (CAF) is a common painful clinical disease and its pathogenesis remains poorly understood. After failure of pharmacological therapy, that is the first-line treatment, surgical sphincterotomy remains the treatment of choice although it is followed by a high rate of anal incontinence resulting from the sphincter damage; therefore, the research of a sphincter-saving surgical option has become an important goal. The aim of this study was to evaluate the manometric modifications and the incidence of anal incontinence after fissurectomy and anoplasty with advancement skin flap in patients affected by CAF with hypertonia of the internal anal sphincter (IAS). Fifteen patients affected by CAF with hypertonia of IAS, unresponsive to medical therapy, were enrolled. All subjects underwent fissurectomy and anoplasty with advancement skin flap. Anorectal manometry was performed preoperatively and after 6 and 12 months from surgery. Maximum resting pressure (MRP), maximum squeeze pressure (MSP), ultraslow wave activity (USWA), fissure healing, anal continence, and postoperative complications were recorded. All patients healed within 30 days from surgery. No intra- or postoperative complications were recorded except for a case of partial donor site break. No significant modifications of MSP were detected. Six months after surgery, MRP was higher with respect to healthy subjects but significantly reduced in comparison to baseline levels. At 12 months, it was higher have versus 6-month values but significantly lower versus preoperative values. USWA was significantly represented in patients with CAF versus healthy subject. Both at 6 and 12 months, they decreased significantly with respect to preoperative values without significant differences versus healthy subjects. Both at 6 and 12 months, anal continence did not differ with respect to preoperative time. The fissurectomy with anoplasty resulted in a high healing rate without surgical sequelae or anal incontinence. Also, it was able to reduce IAS pressure in the same manner as surgical sphincterotomy or forceful dilatation.