Chilean sick leave revolves around one document: the licencia médica. It is issued by a doctor, submitted electronically, and then approved, reduced, or rejected by a third party — COMPIN for FONASA members, or the employee’s ISAPRE. The employer’s role sits in the middle of that chain, and getting the submission timing wrong is what costs employees their subsidy.
This guide covers Chilean sick leave in 2026: the three-day rule, who actually pays, the approval process, the submission deadlines, and the job protection that runs alongside.
Key takeaways
- Sick leave requires a licencia médica, now issued electronically (LME) in the great majority of cases.
- Leave of more than 10 days is paid from day one; leave of 10 days or fewer has a 3-day waiting period (carencia).
- The subsidy (subsidio por incapacidad laboral, SIL) is paid by the health system — FONASA/COMPIN or the employee’s ISAPRE — not by the employer.
- The subsidy is based on the average of the last 3 months of taxable earnings, subject to a cap.
- Employers must forward the licencia within statutory deadlines, and cannot dismiss an employee during approved medical leave.
The three-day rule
Chile’s waiting period depends on the length of the leave certified, not on the day count of the absence:
| Length of licencia médica | Payment |
|---|---|
| More than 10 days | Subsidy paid from day 1 |
| 10 days or fewer | First 3 days unpaid; subsidy from day 4 |
This produces a well-known cliff edge: an 11-day licencia is paid in full, while a 10-day licencia loses three days. Doctors are aware of it, and employees on the boundary often ask about it directly.
The rule applies per licencia. Consecutive licencias for the same condition may be treated as continuous where the extension is issued without a break, which removes the second waiting period — but this depends on how the extension is issued and assessed.
Who pays
The subsidy is funded through the health system, based on the employee’s affiliation:
- FONASA members: the subsidy is administered by the relevant Caja de Compensación or the health service, with COMPIN authorising the leave.
- ISAPRE members: the ISAPRE both authorises the leave and pays the subsidy.
The employer does not pay salary during approved medical leave and does not fund the subsidy. What the employer does is continue paying social security contributions on the subsidised amount, and — where the employer has agreed to advance the subsidy — pay the employee and recover from the payer.
The subsidy is calculated on the average taxable remuneration of the last three calendar months before the month the leave starts, subject to the applicable cap. Employees with variable pay in those months therefore see their subsidy move with recent earnings.
Approval: COMPIN and ISAPRE
A licencia médica is not self-executing. The authorising body — COMPIN (Comisión de Medicina Preventiva e Invalidez) for FONASA, or the ISAPRE — reviews it and may:
- Approve it as issued
- Reduce the number of days
- Reject it entirely
Rejection or reduction can be appealed, by the employee, to the Superintendencia de Seguridad Social (SUSESO) in defined circumstances. Where a licencia is rejected, the absence becomes unjustified unless the employee successfully appeals — a significant risk that employers should not compound by treating rejection as automatic misconduct.
The employer also has a role: it can raise observations on a licencia, and it must record the employee’s contractual and contribution data accurately, because errors there are a frequent cause of rejection or delay.
Submission deadlines
Timing is where most practical problems arise. Under the licencia médica regulations:
- The employee must submit the licencia to the employer within 2 working days of the start of the leave (3 days for non-dependent workers, with longer periods in some cases).
- The employer must then forward it to the authorising body within 3 working days of receiving it.
With the electronic licencia (LME), much of this happens through the platform, and the employer’s step is completed online. But the obligation and the deadline remain, and employers who leave the LME queue unattended for a week routinely cause their employees’ subsidies to be delayed or questioned.
Job protection
Article 161 of the Labour Code expressly prohibits terminating an employee on the grounds of company needs (necesidades de la empresa) while the employee is on medical leave. Termination on other statutory grounds is not automatically barred, but dismissing during approved medical leave invites close scrutiny and, where the real reason is the absence, a finding of unjustified dismissal.
Chile has no fixed limit on the duration of medical leave. Prolonged incapacity is instead resolved through the disability pension route: where the condition is permanent, the employee is assessed for an invalidity pension by the relevant commission, and the employment is then addressed on that basis.
Work accidents: Law 16.744
Absence caused by a work accident or occupational disease is not ordinary medical leave. It falls under Law 16.744 and is handled by the employer’s occupational safety insurer — a mutualidad (ACHS, Mutual de Seguridad, IST) or the Instituto de Seguridad Laboral.
Under that regime the employee receives 100% of the base remuneration from day one, with no waiting period, plus full medical treatment at no cost. Employers must report the accident to the insurer immediately. Sending an injured employee through the ordinary licencia route denies them the better benefit and leaves the mutualidad’s cover unused.
Employer obligations
Chilean employers have six core duties:
- Receive and forward the licencia médica within the statutory deadline, through the LME platform where applicable.
- Provide accurate remuneration and contribution data so the subsidy is calculated correctly.
- Continue paying social security contributions during the subsidised period.
- Not dismiss for company needs while the employee is on medical leave.
- Report work accidents to the mutualidad so Law 16.744 benefits apply instead of ordinary leave.
- Reinstate the employee at the end of the certified leave.
Common pitfalls
1. Sitting on the licencia
The employer’s three-working-day forwarding deadline is short and the consequence — a delayed or rejected subsidy — falls on the employee. Unattended LME queues are the single most common Chilean sick leave failure.
2. Paying salary instead of the subsidy without an arrangement
Employers who simply keep paying salary during medical leave, without an agreed advance-and-recover arrangement, often find recovery difficult and the accounting messy.
3. Treating a rejected licencia as automatic misconduct
Rejection can be appealed to SUSESO. Moving straight to disciplinary action before the appeal route is exhausted is premature and frequently reversed.
4. Misapplying the three-day rule
The waiting period depends on whether the licencia is for more than 10 days, not on how many days the employee ends up absent. Applying carencia to an 11-day licencia underpays.
5. Routing work injuries through ordinary licencias
Law 16.744 pays 100% from day one with no waiting period. Using the ordinary route costs the employee money and bypasses insurance the employer already funds.
For more Chilean context, see our guide to annual leave entitlement in Chile, the overview of the main types of leave employers manage, and our guide to absence management.
Frequently asked questions
Does the employer pay sick leave in Chile?
No. The subsidy is paid through FONASA/COMPIN or the employee’s ISAPRE. The employer forwards the licencia, supplies accurate pay data, and continues social security contributions.
What is the three-day rule?
Licencias of 10 days or fewer have a three-day waiting period, with the subsidy starting on day four. Licencias of more than 10 days are paid from day one.
How is the subsidy calculated?
On the average taxable remuneration of the three calendar months before the month the leave starts, subject to the statutory cap.
What happens if a licencia is rejected?
The absence is unjustified unless the employee appeals successfully. Rejections and reductions can be appealed to SUSESO, so employers should not treat rejection as a final answer.
Can an employee be dismissed while on medical leave?
Not on the grounds of company needs — the Labour Code prohibits it expressly. Other grounds are not automatically barred but are scrutinised closely.
Is there a maximum length of medical leave?
No fixed statutory limit. Long-term incapacity is resolved through disability pension assessment rather than a time cap on the leave itself.
Putting it into practice
Five checks cover most Chilean sick leave risk:
- Assign clear ownership of the LME queue with a service level well inside the three-working-day deadline.
- Verify that remuneration and contribution data sent with each licencia matches payroll records.
- Configure the carencia rule on licencia length, not on absence length.
- Create a separate Law 16.744 absence type for work accidents and route them to the mutualidad first.
- Block termination on company-needs grounds while a medical leave is open in the system.
A leave management system that tracks each licencia through submission, forwarding, and authorisation — and flags the ones sitting past two days — turns Chile’s approval chain from a source of employee income gaps into a routine workflow.
Sources
- Superintendencia de Seguridad Social (SUSESO) — licencias médicas (primary source)
- Dirección del Trabajo — Chilean Labour Code guidance
- Law 16.744 on occupational accidents and diseases
Last updated: 26 July 2026. This article is general guidance, not legal advice. Subsidy caps and calculation rules are revised periodically — confirm current figures with SUSESO or the relevant ISAPRE.