Below is a one-stop, Philippine-specific legal explainer on holiday pay while an employee is on study leave. I have organised it so you can (1) see the basic legal texts, (2) understand how the two benefits interact in government and in the private sector, (3) apply the correct computation, and (4) spot the practical issues that HR, payroll and employees usually miss.

1. Two different benefits, two different legal bases

Benefit	Core statute / rule	Who is covered?	Nature of the benefit
Holiday pay	Art. 94 (Labor Code) + Book III, Rule IV of the Omnibus Rules	Private-sector “rank-and-file” employees who are daily-paid; monthly-paid workers already receive pay for un-worked regular holidays	Pay equal to 100 % of the basic daily wage for an un-worked regular holiday; higher rates when the employee works on a holiday
Study leave	§ 68, Rule XVI, Omnibus Rules on Leave (EO 292); CSC MC 14-1999 as amended by MC 21-2004 & MC 05-2021	Career government personnel only (teachers have their own rule under the Magna Carta for Teachers)	Up to 6 months leave with pay to finish a master’s thesis/prepare for the bar/board; subject to strict eligibility & return-service obligations

(Wikipedia, Civil Service Commission, E-Library)

Key point: For the private sector, “study leave” is not a statutory entitlement at all—it exists only if granted by company policy, Collective Bargaining Agreement (CBA) or a scholarship contract. For government workers it is a codified, paid leave.

2. How holiday pay applies while on study leave

2.1 Government sector

Government employees are paid on a monthly-salary basis. Under the General Appropriations Act and the Position Classification System, a monthly salary already covers Saturdays, Sundays and all regular/special holidays.
Because study leave is with pay by definition, the employee’s salary continues to run during the leave period, and holidays that fall within it are simply part of the monthly pay—there is no separate “holiday-pay” computation required.
The only caveat is that the agency must have an approved Study-Leave Contract (CSC-prescribed form) and the employee must render the return-service obligation (minimum six months for ≤ 1 month of leave; two to three years where the leave is 2-6 months). (Civil Service Commission, Civil Service Commission)

2.2 Private sector

Because the Labor Code’s holiday-pay rule hinges on the employee being “present or on leave with pay on the work-day immediately preceding the holiday,” two scenarios emerge:

Scenario	Entitlement
Study leave WITH pay (granted by company/CBA)	Employee is deemed “on leave with pay”, so holiday pay must still be paid for every regular holiday inside the leave period. If the company normally treats study-leave days as paid rest days, the daily wage for the holiday is still owed. (library.laborlaw.ph, Labor Law Philippines)
Study leave WITHOUT pay (no company benefit)	Employee is not “on leave with pay” on the day immediately before the holiday, so no holiday-pay is due (“no work, no pay” principle). The holiday can be paid only if the CBA or company practice says so. (library.laborlaw.ph, Labor Law Philippines)

3. Computation guide (private sector)

Step-by-step example Employee is daily-paid at ₱650 basic wage, on a 15-day paid study leave granted under a CBA.

Regular holiday (e.g., Independence Day) falls inside the leave.
Because the leave is paid, the employee gets 100 % of ₱650 = ₱650 for that un-worked day.
If the employer also requires her to work that day, pay becomes 200 % of the basic wage for the first 8 hrs, i.e., ₱1 300, plus the usual overtime premium if applicable. (Wikipedia, library.laborlaw.ph)

(For monthly-paid employees, no extra step is needed: the monthly salary already covers the holiday.)

4. Tax and payroll accounting notes

Holiday pay that is part of statutory wages is subject to withholding tax only when the employee’s total taxable income exceeds the threshold in the TRAIN Law.
Because government study leave is salary continuation, it is treated as ordinary compensation income.
Private-sector study-leave pay is likewise ordinary income unless it is paid out of a scholarship grant properly classified as a de minimis benefit under BIR RR 05-2011.

5. Jurisprudence & enforcement snapshot

Case / issuance	Take-away
G.R. No. 233413 (2019) – Supreme Court	Re-affirms that holiday pay is due only when the employee is present or on leave with pay on the day immediately preceding the holiday. (Lawphil)
2023 DOLE Handbook on Statutory Monetary Benefits	Clarifies that employees “on leave of absence with pay” are covered by Art. 94 holiday-pay rule. (library.laborlaw.ph)
CSC MC 21-2004	Amends § 68, Rule XVI to codify a six-month cap and return-service periods for paid study leave. (Civil Service Commission)

Non-compliance complaints go to:

DOLE Regional Office / NLRC – private sector (Art. 128 inspection or money claim).
CSC / Ombudsman – government sector (for misuse of study-leave funds or failure to execute the return-service contract).

6. HR & employee compliance checklist

Check the contract – Is the study leave expressly with or without pay?
Confirm the day-before-holiday status – Payroll must tag the employee as “SL-P” (study leave with pay) in the time-keeping system; otherwise the holiday-pay module will skip payment.
Secure the CSC Study-Leave Contract (government) or HR scholarship agreement (private) before the leave starts.
Record the return-service balance – Government agencies must monitor fulfilment; private employers may bind the employee through liquidated-damages clauses if training costs were advanced.
Disclose in payslips – Show a separate line for “Holiday Pay” to comply with the Payslip Law (RA 11210) and NLRC evidentiary rules.

7. Frequently-asked questions

Question	Short answer
Can a government employee take study leave for less than one month?	Yes, but CSC MC 21-2004 still imposes the minimum 6-month return service even for shorter leaves. (Civil Service Commission)
Does a special non-working holiday inside the study-leave period have to be paid?	Only if the company or agency policy says so; under DOLE pay rules special holidays follow “no work, no pay.” (Wikipedia)
Is holiday pay waived if the employee receives a scholarship allowance?	No; statutory holiday pay cannot be waived (Art. 100, non-diminution). The allowance is separate unless the CBA clearly off-sets it.

Bottom line

In the Philippines, holiday pay follows the simple rule “present or on leave with pay.” A paid study leave therefore does not interrupt an employee’s entitlement to holiday pay (private sector) or monthly salary (government). Conversely, an unpaid study leave breaks the “with pay” condition, so no holiday pay attaches unless a more generous company or agency rule applies.

Keep the leave contract clear, tag the payroll correctly, and the interaction between these two benefits remains straightforward.